Multiple sequence alignment - TraesCS4A01G150200

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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 TraesCS4A01G150200 chr4A 100.000 2627 0 0 1 2627 295132491 295135117 0.000000e+00 4852.0
1 TraesCS4A01G150200 chr4A 83.080 461 44 12 1104 1530 154934516 154934976 3.170000e-104 388.0
2 TraesCS4A01G150200 chr3A 92.852 1441 80 10 679 2114 739289792 739288370 0.000000e+00 2069.0
3 TraesCS4A01G150200 chr3A 94.004 517 25 3 2115 2627 739287805 739287291 0.000000e+00 778.0
4 TraesCS4A01G150200 chr3A 83.240 358 40 12 301 654 745941688 745942029 7.060000e-81 311.0
5 TraesCS4A01G150200 chr3B 87.052 1143 89 24 301 1443 685848790 685849873 0.000000e+00 1236.0
6 TraesCS4A01G150200 chr3B 94.461 668 36 1 1441 2108 685861466 685862132 0.000000e+00 1027.0
7 TraesCS4A01G150200 chr3B 90.716 517 41 4 2115 2627 277085612 277085099 0.000000e+00 682.0
8 TraesCS4A01G150200 chr3B 93.622 439 22 4 2115 2547 685862706 685863144 0.000000e+00 651.0
9 TraesCS4A01G150200 chr3B 83.883 273 25 7 300 562 728492071 728491808 2.610000e-60 243.0
10 TraesCS4A01G150200 chr3B 78.595 299 33 22 301 596 749159618 749159888 4.500000e-38 169.0
11 TraesCS4A01G150200 chr1A 84.178 493 45 11 1144 1603 426928179 426927687 5.160000e-122 448.0
12 TraesCS4A01G150200 chr1A 90.728 151 13 1 1613 1763 426927626 426927477 1.590000e-47 200.0
13 TraesCS4A01G150200 chr2A 82.836 536 55 15 1104 1603 733290260 733290794 1.860000e-121 446.0
14 TraesCS4A01G150200 chr2A 91.447 152 11 2 1613 1763 733290855 733291005 9.530000e-50 207.0
15 TraesCS4A01G150200 chr6B 82.649 536 55 15 1104 1602 459794191 459794725 8.630000e-120 440.0
16 TraesCS4A01G150200 chr6B 84.026 313 22 8 1318 1603 459794830 459795141 2.580000e-70 276.0
17 TraesCS4A01G150200 chr6B 80.528 303 29 18 301 600 710144891 710145166 3.430000e-49 206.0
18 TraesCS4A01G150200 chr6B 91.275 149 12 1 1613 1761 459795202 459795349 4.430000e-48 202.0
19 TraesCS4A01G150200 chr2B 81.550 542 58 17 1104 1603 408323296 408322755 2.430000e-110 409.0
20 TraesCS4A01G150200 chr2B 83.824 272 25 9 301 562 184638215 184638477 9.400000e-60 241.0
21 TraesCS4A01G150200 chr2B 81.212 330 32 9 307 633 53569812 53570114 3.380000e-59 239.0
22 TraesCS4A01G150200 chr2B 83.577 274 26 7 299 562 148408214 148407950 3.380000e-59 239.0
23 TraesCS4A01G150200 chr2B 85.020 247 16 5 1362 1587 408326292 408326046 5.650000e-57 231.0
24 TraesCS4A01G150200 chr2B 89.809 157 9 3 1613 1763 408322694 408322539 7.420000e-46 195.0
25 TraesCS4A01G150200 chr2B 89.241 158 9 4 1613 1763 408324994 408324838 9.600000e-45 191.0
26 TraesCS4A01G150200 chr1D 85.223 291 27 8 2 283 328182808 328183091 4.280000e-73 285.0
27 TraesCS4A01G150200 chr6A 82.216 343 31 14 301 640 514356234 514355919 4.310000e-68 268.0
28 TraesCS4A01G150200 chr6A 90.270 185 16 2 300 483 420386898 420386715 9.400000e-60 241.0
29 TraesCS4A01G150200 chr6A 80.606 330 37 16 301 630 430571848 430571546 2.030000e-56 230.0
30 TraesCS4A01G150200 chr6A 90.141 71 6 1 584 653 564512207 564512277 1.000000e-14 91.6
31 TraesCS4A01G150200 chr7B 81.337 359 36 18 297 651 504220948 504221279 2.010000e-66 263.0
32 TraesCS4A01G150200 chr4B 81.461 356 35 17 301 652 159644170 159643842 2.010000e-66 263.0
33 TraesCS4A01G150200 chr7A 82.902 193 21 7 308 496 83129779 83129963 2.090000e-36 163.0
34 TraesCS4A01G150200 chr3D 88.333 120 11 2 580 699 238580801 238580685 9.800000e-30 141.0
35 TraesCS4A01G150200 chr1B 85.714 133 11 7 521 651 316260871 316260997 1.640000e-27 134.0


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 TraesCS4A01G150200 chr4A 295132491 295135117 2626 False 4852.0 4852 100.000000 1 2627 1 chr4A.!!$F2 2626
1 TraesCS4A01G150200 chr3A 739287291 739289792 2501 True 1423.5 2069 93.428000 679 2627 2 chr3A.!!$R1 1948
2 TraesCS4A01G150200 chr3B 685848790 685849873 1083 False 1236.0 1236 87.052000 301 1443 1 chr3B.!!$F1 1142
3 TraesCS4A01G150200 chr3B 685861466 685863144 1678 False 839.0 1027 94.041500 1441 2547 2 chr3B.!!$F3 1106
4 TraesCS4A01G150200 chr3B 277085099 277085612 513 True 682.0 682 90.716000 2115 2627 1 chr3B.!!$R1 512
5 TraesCS4A01G150200 chr1A 426927477 426928179 702 True 324.0 448 87.453000 1144 1763 2 chr1A.!!$R1 619
6 TraesCS4A01G150200 chr2A 733290260 733291005 745 False 326.5 446 87.141500 1104 1763 2 chr2A.!!$F1 659
7 TraesCS4A01G150200 chr6B 459794191 459795349 1158 False 306.0 440 85.983333 1104 1761 3 chr6B.!!$F2 657
8 TraesCS4A01G150200 chr2B 408322539 408326292 3753 True 256.5 409 86.405000 1104 1763 4 chr2B.!!$R2 659

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
53 54 0.325390 AACCGAAGTAGGAGAGGGGG 60.325 60.0 0.0 0.0 34.73 5.40 F
502 503 0.462759 CCTTTCTCCCGCATGACCTC 60.463 60.0 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 3278 1.967779 GGGCAAACAACTACCAACCAT 59.032 47.619 0.00 0.0 0.0 3.55 R
2276 5265 0.679640 CTGCCCGGCCAAAGTCATTA 60.680 55.000 7.03 0.0 0.0 1.90 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
17 18 4.284550 AGCATGGCCGGTTGTGGT 62.285 61.111 1.90 1.84 0.00 4.16
18 19 4.054825 GCATGGCCGGTTGTGGTG 62.055 66.667 1.90 0.00 0.00 4.17
19 20 4.054825 CATGGCCGGTTGTGGTGC 62.055 66.667 1.90 0.00 0.00 5.01
24 25 3.645975 CCGGTTGTGGTGCACGTC 61.646 66.667 11.45 6.85 37.14 4.34
25 26 2.892914 CGGTTGTGGTGCACGTCA 60.893 61.111 11.45 9.57 37.14 4.35
27 28 1.063488 GGTTGTGGTGCACGTCAAC 59.937 57.895 30.21 30.21 37.14 3.18
29 30 2.465299 TTGTGGTGCACGTCAACGG 61.465 57.895 17.25 0.00 44.95 4.44
32 33 2.029369 GGTGCACGTCAACGGGTA 59.971 61.111 11.45 0.00 46.07 3.69
33 34 2.025418 GGTGCACGTCAACGGGTAG 61.025 63.158 11.45 0.00 46.07 3.18
34 35 1.007038 GTGCACGTCAACGGGTAGA 60.007 57.895 0.00 0.00 46.07 2.59
35 36 0.598158 GTGCACGTCAACGGGTAGAA 60.598 55.000 0.00 0.00 46.07 2.10
36 37 0.598158 TGCACGTCAACGGGTAGAAC 60.598 55.000 6.66 0.00 46.07 3.01
37 38 1.287041 GCACGTCAACGGGTAGAACC 61.287 60.000 6.66 0.00 46.07 3.62
48 49 3.010200 GGGTAGAACCGAAGTAGGAGA 57.990 52.381 0.00 0.00 39.83 3.71
49 50 2.950975 GGGTAGAACCGAAGTAGGAGAG 59.049 54.545 0.00 0.00 39.83 3.20
50 51 2.950975 GGTAGAACCGAAGTAGGAGAGG 59.049 54.545 0.00 0.00 34.73 3.69
51 52 2.146920 AGAACCGAAGTAGGAGAGGG 57.853 55.000 0.00 0.00 34.73 4.30
52 53 1.112950 GAACCGAAGTAGGAGAGGGG 58.887 60.000 0.00 0.00 34.73 4.79
53 54 0.325390 AACCGAAGTAGGAGAGGGGG 60.325 60.000 0.00 0.00 34.73 5.40
68 69 2.768769 GGGGAGGGGACTGTAGGC 60.769 72.222 0.00 0.00 44.43 3.93
69 70 3.155167 GGGAGGGGACTGTAGGCG 61.155 72.222 0.00 0.00 44.43 5.52
71 72 3.851128 GAGGGGACTGTAGGCGGC 61.851 72.222 0.00 0.00 44.43 6.53
72 73 4.715130 AGGGGACTGTAGGCGGCA 62.715 66.667 13.08 0.00 41.13 5.69
73 74 4.162690 GGGGACTGTAGGCGGCAG 62.163 72.222 13.08 1.84 39.67 4.85
75 76 2.663196 GGACTGTAGGCGGCAGTT 59.337 61.111 13.08 0.00 45.99 3.16
76 77 1.448013 GGACTGTAGGCGGCAGTTC 60.448 63.158 13.08 11.49 45.99 3.01
77 78 1.292223 GACTGTAGGCGGCAGTTCA 59.708 57.895 13.08 3.53 45.99 3.18
78 79 1.004918 ACTGTAGGCGGCAGTTCAC 60.005 57.895 13.08 1.17 43.87 3.18
79 80 1.741770 CTGTAGGCGGCAGTTCACC 60.742 63.158 13.08 0.00 0.00 4.02
81 82 1.741770 GTAGGCGGCAGTTCACCAG 60.742 63.158 13.08 0.00 0.00 4.00
82 83 2.954684 TAGGCGGCAGTTCACCAGG 61.955 63.158 13.08 0.00 0.00 4.45
85 86 2.669569 CGGCAGTTCACCAGGGTG 60.670 66.667 12.29 12.29 46.64 4.61
88 89 1.604593 GCAGTTCACCAGGGTGCAT 60.605 57.895 13.64 0.00 45.04 3.96
90 91 1.075482 AGTTCACCAGGGTGCATGG 59.925 57.895 13.64 3.18 45.04 3.66
91 92 1.978617 GTTCACCAGGGTGCATGGG 60.979 63.158 13.64 2.42 45.04 4.00
92 93 3.884704 TTCACCAGGGTGCATGGGC 62.885 63.158 13.64 0.00 45.04 5.36
93 94 4.371417 CACCAGGGTGCATGGGCT 62.371 66.667 9.58 0.00 42.48 5.19
97 98 3.736224 AGGGTGCATGGGCTGGAG 61.736 66.667 0.00 0.00 41.91 3.86
98 99 4.828296 GGGTGCATGGGCTGGAGG 62.828 72.222 0.00 0.00 41.91 4.30
99 100 4.052518 GGTGCATGGGCTGGAGGT 62.053 66.667 0.00 0.00 41.91 3.85
100 101 2.753043 GTGCATGGGCTGGAGGTG 60.753 66.667 0.00 0.00 41.91 4.00
101 102 4.051167 TGCATGGGCTGGAGGTGG 62.051 66.667 0.00 0.00 41.91 4.61
103 104 4.828296 CATGGGCTGGAGGTGGGC 62.828 72.222 0.00 0.00 0.00 5.36
162 163 4.329545 GCAGGGTGGAGTTGGCGA 62.330 66.667 0.00 0.00 0.00 5.54
163 164 2.671070 CAGGGTGGAGTTGGCGAT 59.329 61.111 0.00 0.00 0.00 4.58
164 165 1.746615 CAGGGTGGAGTTGGCGATG 60.747 63.158 0.00 0.00 0.00 3.84
166 167 1.303317 GGGTGGAGTTGGCGATGTT 60.303 57.895 0.00 0.00 0.00 2.71
167 168 0.893727 GGGTGGAGTTGGCGATGTTT 60.894 55.000 0.00 0.00 0.00 2.83
170 171 0.953471 TGGAGTTGGCGATGTTTCGG 60.953 55.000 0.00 0.00 45.59 4.30
171 172 1.644786 GGAGTTGGCGATGTTTCGGG 61.645 60.000 0.00 0.00 45.59 5.14
172 173 1.644786 GAGTTGGCGATGTTTCGGGG 61.645 60.000 0.00 0.00 45.59 5.73
173 174 1.969589 GTTGGCGATGTTTCGGGGT 60.970 57.895 0.00 0.00 45.59 4.95
174 175 1.969064 TTGGCGATGTTTCGGGGTG 60.969 57.895 0.00 0.00 45.59 4.61
175 176 3.131478 GGCGATGTTTCGGGGTGG 61.131 66.667 0.00 0.00 45.59 4.61
176 177 3.131478 GCGATGTTTCGGGGTGGG 61.131 66.667 0.00 0.00 45.59 4.61
177 178 2.437716 CGATGTTTCGGGGTGGGG 60.438 66.667 0.00 0.00 41.74 4.96
179 180 1.613061 GATGTTTCGGGGTGGGGAT 59.387 57.895 0.00 0.00 0.00 3.85
180 181 0.751643 GATGTTTCGGGGTGGGGATG 60.752 60.000 0.00 0.00 0.00 3.51
181 182 2.754254 GTTTCGGGGTGGGGATGC 60.754 66.667 0.00 0.00 0.00 3.91
182 183 4.418328 TTTCGGGGTGGGGATGCG 62.418 66.667 0.00 0.00 0.00 4.73
193 194 3.880846 GGATGCGCCGCAAAGGAG 61.881 66.667 18.69 0.00 43.62 3.69
194 195 3.880846 GATGCGCCGCAAAGGAGG 61.881 66.667 18.69 0.00 43.62 4.30
202 203 3.373565 GCAAAGGAGGCGGGGTTG 61.374 66.667 0.00 0.00 0.00 3.77
203 204 2.676471 CAAAGGAGGCGGGGTTGG 60.676 66.667 0.00 0.00 0.00 3.77
204 205 3.979497 AAAGGAGGCGGGGTTGGG 61.979 66.667 0.00 0.00 0.00 4.12
216 217 4.424711 GTTGGGGGAGGCGATGCA 62.425 66.667 0.00 0.00 0.00 3.96
217 218 4.113815 TTGGGGGAGGCGATGCAG 62.114 66.667 0.00 0.00 0.00 4.41
279 280 4.918201 GCGGAGGAGGCGGGATTG 62.918 72.222 0.00 0.00 0.00 2.67
280 281 4.241555 CGGAGGAGGCGGGATTGG 62.242 72.222 0.00 0.00 0.00 3.16
281 282 3.878667 GGAGGAGGCGGGATTGGG 61.879 72.222 0.00 0.00 0.00 4.12
282 283 3.878667 GAGGAGGCGGGATTGGGG 61.879 72.222 0.00 0.00 0.00 4.96
290 291 3.825623 GGGATTGGGGGCCAGGAG 61.826 72.222 4.39 0.00 33.81 3.69
291 292 3.825623 GGATTGGGGGCCAGGAGG 61.826 72.222 4.39 0.00 33.81 4.30
292 293 3.825623 GATTGGGGGCCAGGAGGG 61.826 72.222 4.39 0.00 33.81 4.30
314 315 3.243002 GGCGACACATCTACTACCACTAC 60.243 52.174 0.00 0.00 0.00 2.73
327 328 6.936968 ACTACCACTACAAAAGGAAGAGAT 57.063 37.500 0.00 0.00 0.00 2.75
347 348 5.128919 AGATGGGCAGATCTAAACAATCAC 58.871 41.667 0.00 0.00 30.50 3.06
350 351 4.883585 TGGGCAGATCTAAACAATCACATC 59.116 41.667 0.00 0.00 0.00 3.06
361 362 9.192642 TCTAAACAATCACATCCATTCATCATT 57.807 29.630 0.00 0.00 0.00 2.57
378 379 9.827198 ATTCATCATTAAAATCTAATGGCCCTA 57.173 29.630 0.00 0.00 36.03 3.53
380 381 9.653516 TCATCATTAAAATCTAATGGCCCTAAA 57.346 29.630 0.00 0.00 36.03 1.85
387 388 6.536684 AATCTAATGGCCCTAAATCCTTCT 57.463 37.500 0.00 0.00 0.00 2.85
396 397 5.105877 GGCCCTAAATCCTTCTGTGTTTAAC 60.106 44.000 0.00 0.00 0.00 2.01
420 421 1.960689 ACCAACCACACATTAAGCCAC 59.039 47.619 0.00 0.00 0.00 5.01
421 422 1.959985 CCAACCACACATTAAGCCACA 59.040 47.619 0.00 0.00 0.00 4.17
422 423 2.030007 CCAACCACACATTAAGCCACAG 60.030 50.000 0.00 0.00 0.00 3.66
430 431 2.165641 ACATTAAGCCACAGTCGATCGA 59.834 45.455 15.15 15.15 0.00 3.59
448 449 2.715532 GATCGCTAATCTGCCCCGCA 62.716 60.000 0.00 0.00 36.92 5.69
449 450 2.116983 ATCGCTAATCTGCCCCGCAT 62.117 55.000 0.00 0.00 38.13 4.73
488 489 2.434359 CGCACGACCTCCCCTTTC 60.434 66.667 0.00 0.00 0.00 2.62
489 490 2.943978 CGCACGACCTCCCCTTTCT 61.944 63.158 0.00 0.00 0.00 2.52
490 491 1.079057 GCACGACCTCCCCTTTCTC 60.079 63.158 0.00 0.00 0.00 2.87
491 492 1.597461 CACGACCTCCCCTTTCTCC 59.403 63.158 0.00 0.00 0.00 3.71
492 493 1.612739 ACGACCTCCCCTTTCTCCC 60.613 63.158 0.00 0.00 0.00 4.30
493 494 2.722201 CGACCTCCCCTTTCTCCCG 61.722 68.421 0.00 0.00 0.00 5.14
494 495 3.009714 ACCTCCCCTTTCTCCCGC 61.010 66.667 0.00 0.00 0.00 6.13
495 496 3.009115 CCTCCCCTTTCTCCCGCA 61.009 66.667 0.00 0.00 0.00 5.69
500 501 1.452108 CCCTTTCTCCCGCATGACC 60.452 63.158 0.00 0.00 0.00 4.02
501 502 1.604378 CCTTTCTCCCGCATGACCT 59.396 57.895 0.00 0.00 0.00 3.85
502 503 0.462759 CCTTTCTCCCGCATGACCTC 60.463 60.000 0.00 0.00 0.00 3.85
503 504 0.462759 CTTTCTCCCGCATGACCTCC 60.463 60.000 0.00 0.00 0.00 4.30
504 505 0.909610 TTTCTCCCGCATGACCTCCT 60.910 55.000 0.00 0.00 0.00 3.69
505 506 0.909610 TTCTCCCGCATGACCTCCTT 60.910 55.000 0.00 0.00 0.00 3.36
512 513 1.494960 GCATGACCTCCTTCTCCTCT 58.505 55.000 0.00 0.00 0.00 3.69
577 578 4.052229 CGAGCCACGGGAAGTCGT 62.052 66.667 0.00 0.00 44.91 4.34
725 726 4.373116 GCTGTTCACCGCCTCCGA 62.373 66.667 0.00 0.00 36.29 4.55
759 782 4.767255 CCGCCACTCTGCCTCCAC 62.767 72.222 0.00 0.00 0.00 4.02
763 786 1.077930 CCACTCTGCCTCCACCATG 60.078 63.158 0.00 0.00 0.00 3.66
765 788 2.124403 CTCTGCCTCCACCATGCC 60.124 66.667 0.00 0.00 0.00 4.40
766 789 4.100084 TCTGCCTCCACCATGCCG 62.100 66.667 0.00 0.00 0.00 5.69
772 795 4.408821 TCCACCATGCCGCCACTC 62.409 66.667 0.00 0.00 0.00 3.51
792 815 1.687494 CGCTGGAGTCGCAAGTAAGC 61.687 60.000 0.00 0.00 39.48 3.09
814 837 6.279882 AGCTTCTATTGCTGAACTCATCTAC 58.720 40.000 0.00 0.00 39.56 2.59
977 1012 4.093291 CCGCTCAGCTTGGCCTCT 62.093 66.667 3.32 0.00 0.00 3.69
1128 3022 6.538742 CGGTTATGGTGAGATTGAAACTACAT 59.461 38.462 0.00 0.00 0.00 2.29
1171 3073 4.683832 GCGTCTCATTTTCTTCTAGGCTA 58.316 43.478 0.00 0.00 0.00 3.93
1172 3074 4.742659 GCGTCTCATTTTCTTCTAGGCTAG 59.257 45.833 15.56 15.56 0.00 3.42
1184 3086 9.988815 TTTCTTCTAGGCTAGATATTCATTGAC 57.011 33.333 24.06 0.00 34.22 3.18
1283 3199 4.219115 TCCTAATCAACCAGTTTGGCAAA 58.781 39.130 8.93 8.93 42.67 3.68
1334 3250 5.061179 GGAGCTGAACAACCTTTTACAGTA 58.939 41.667 0.00 0.00 0.00 2.74
1353 3278 7.956328 ACAGTATCCACTCTCACAAATACTA 57.044 36.000 0.00 0.00 30.46 1.82
1667 4078 6.384886 AGCCACCAAATCATGATCCTTTAATT 59.615 34.615 9.06 0.00 0.00 1.40
1801 4219 7.188468 TGTTTGCTATTTCCTGCAATTTTTC 57.812 32.000 0.00 0.00 46.55 2.29
1817 4235 7.447853 TGCAATTTTTCCCTTTTATTTCTGCAT 59.552 29.630 0.00 0.00 0.00 3.96
1877 4295 2.837498 TCCATATGCAATCTGTGGACG 58.163 47.619 0.50 0.00 34.23 4.79
1887 4305 1.616159 TCTGTGGACGATCACACTCA 58.384 50.000 10.49 0.00 42.05 3.41
1940 4358 3.746492 ACTTGTCAGCTACCTTTAAAGCG 59.254 43.478 9.86 5.99 43.63 4.68
1961 4379 4.781528 GCGAATGTGACGATGAAAACTTAC 59.218 41.667 0.00 0.00 0.00 2.34
2032 4450 3.741388 GCTAAGCCAGCGAGGATAAAAGA 60.741 47.826 2.12 0.00 41.37 2.52
2047 4465 5.939883 GGATAAAAGATTGCCTTGCCTTTTT 59.060 36.000 0.00 0.00 38.99 1.94
2055 4473 3.540617 TGCCTTGCCTTTTTCCTTTTTC 58.459 40.909 0.00 0.00 0.00 2.29
2057 4475 3.809832 GCCTTGCCTTTTTCCTTTTTCTC 59.190 43.478 0.00 0.00 0.00 2.87
2061 4479 6.183360 CCTTGCCTTTTTCCTTTTTCTCTGTA 60.183 38.462 0.00 0.00 0.00 2.74
2065 4483 6.039382 GCCTTTTTCCTTTTTCTCTGTACTGA 59.961 38.462 2.21 2.21 0.00 3.41
2082 4500 4.094830 ACTGATAAGAACCCGGTTGTTT 57.905 40.909 17.19 9.40 31.63 2.83
2088 4506 0.956633 GAACCCGGTTGTTTTCCTCC 59.043 55.000 7.78 0.00 0.00 4.30
2109 4527 3.392616 CCTCTCATGGCCCTGTTAAGTAT 59.607 47.826 7.98 0.00 0.00 2.12
2209 5198 3.544834 CCGCTGAGAACTTCATTTATGCG 60.545 47.826 0.00 0.00 42.03 4.73
2212 5201 4.497006 GCTGAGAACTTCATTTATGCGCAT 60.497 41.667 28.23 28.23 34.68 4.73
2284 5273 1.407437 CCCCGAGCTTGCTAATGACTT 60.407 52.381 0.00 0.00 0.00 3.01
2285 5274 2.359900 CCCGAGCTTGCTAATGACTTT 58.640 47.619 0.00 0.00 0.00 2.66
2409 5398 4.748277 TCTCTGATTGCTGATGATGTGA 57.252 40.909 0.00 0.00 0.00 3.58
2559 5549 8.064222 CGAGTTTATTATACTGTGAGCAATTGG 58.936 37.037 7.72 0.00 0.00 3.16
2599 5589 4.422057 TCAGTTATGGGTTAGTGAGGACA 58.578 43.478 0.00 0.00 0.00 4.02
2609 5599 0.609131 AGTGAGGACAAATTGGGGCG 60.609 55.000 0.00 0.00 0.00 6.13
2616 5606 2.758423 GGACAAATTGGGGCGTAAATCT 59.242 45.455 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.284550 ACCACAACCGGCCATGCT 62.285 61.111 0.00 0.00 0.00 3.79
1 2 4.054825 CACCACAACCGGCCATGC 62.055 66.667 0.00 0.00 0.00 4.06
3 4 4.594854 TGCACCACAACCGGCCAT 62.595 61.111 0.00 0.00 0.00 4.40
7 8 3.645975 GACGTGCACCACAACCGG 61.646 66.667 12.15 0.00 33.40 5.28
8 9 2.465299 TTGACGTGCACCACAACCG 61.465 57.895 12.15 0.00 33.40 4.44
10 11 1.297304 CGTTGACGTGCACCACAAC 60.297 57.895 28.41 28.41 39.08 3.32
11 12 2.465299 CCGTTGACGTGCACCACAA 61.465 57.895 12.15 14.51 37.74 3.33
12 13 2.892914 CCGTTGACGTGCACCACA 60.893 61.111 12.15 8.90 37.74 4.17
13 14 2.974935 TACCCGTTGACGTGCACCAC 62.975 60.000 12.15 6.11 37.74 4.16
14 15 2.702751 CTACCCGTTGACGTGCACCA 62.703 60.000 12.15 0.72 37.74 4.17
16 17 0.598158 TTCTACCCGTTGACGTGCAC 60.598 55.000 6.82 6.82 37.74 4.57
17 18 0.598158 GTTCTACCCGTTGACGTGCA 60.598 55.000 0.00 0.00 37.74 4.57
18 19 1.287041 GGTTCTACCCGTTGACGTGC 61.287 60.000 0.00 0.00 37.74 5.34
19 20 1.005294 CGGTTCTACCCGTTGACGTG 61.005 60.000 0.00 0.00 43.07 4.49
21 22 4.157817 CGGTTCTACCCGTTGACG 57.842 61.111 0.00 0.00 43.07 4.35
29 30 2.950975 CCTCTCCTACTTCGGTTCTACC 59.049 54.545 0.00 0.00 34.05 3.18
30 31 2.950975 CCCTCTCCTACTTCGGTTCTAC 59.049 54.545 0.00 0.00 0.00 2.59
32 33 1.342175 CCCCTCTCCTACTTCGGTTCT 60.342 57.143 0.00 0.00 0.00 3.01
33 34 1.112950 CCCCTCTCCTACTTCGGTTC 58.887 60.000 0.00 0.00 0.00 3.62
34 35 0.325390 CCCCCTCTCCTACTTCGGTT 60.325 60.000 0.00 0.00 0.00 4.44
35 36 1.310373 CCCCCTCTCCTACTTCGGT 59.690 63.158 0.00 0.00 0.00 4.69
36 37 4.279326 CCCCCTCTCCTACTTCGG 57.721 66.667 0.00 0.00 0.00 4.30
50 51 2.040779 CCTACAGTCCCCTCCCCC 60.041 72.222 0.00 0.00 0.00 5.40
51 52 2.768769 GCCTACAGTCCCCTCCCC 60.769 72.222 0.00 0.00 0.00 4.81
52 53 3.155167 CGCCTACAGTCCCCTCCC 61.155 72.222 0.00 0.00 0.00 4.30
53 54 3.155167 CCGCCTACAGTCCCCTCC 61.155 72.222 0.00 0.00 0.00 4.30
54 55 3.851128 GCCGCCTACAGTCCCCTC 61.851 72.222 0.00 0.00 0.00 4.30
56 57 4.162690 CTGCCGCCTACAGTCCCC 62.163 72.222 0.00 0.00 0.00 4.81
57 58 3.391382 ACTGCCGCCTACAGTCCC 61.391 66.667 0.00 0.00 45.06 4.46
61 62 1.741770 GGTGAACTGCCGCCTACAG 60.742 63.158 0.00 0.00 41.08 2.74
62 63 2.345991 GGTGAACTGCCGCCTACA 59.654 61.111 0.00 0.00 34.02 2.74
65 66 4.335647 CCTGGTGAACTGCCGCCT 62.336 66.667 0.00 0.00 37.59 5.52
77 78 4.371417 CAGCCCATGCACCCTGGT 62.371 66.667 4.19 0.00 41.13 4.00
79 80 4.051167 TCCAGCCCATGCACCCTG 62.051 66.667 0.00 0.00 41.13 4.45
81 82 4.828296 CCTCCAGCCCATGCACCC 62.828 72.222 0.00 0.00 41.13 4.61
82 83 4.052518 ACCTCCAGCCCATGCACC 62.053 66.667 0.00 0.00 41.13 5.01
83 84 2.753043 CACCTCCAGCCCATGCAC 60.753 66.667 0.00 0.00 41.13 4.57
85 86 4.828296 CCCACCTCCAGCCCATGC 62.828 72.222 0.00 0.00 37.95 4.06
131 132 3.285215 CTGCCGCCATGCATCTCC 61.285 66.667 0.00 0.00 41.16 3.71
132 133 3.285215 CCTGCCGCCATGCATCTC 61.285 66.667 0.00 0.00 41.16 2.75
133 134 4.889112 CCCTGCCGCCATGCATCT 62.889 66.667 0.00 0.00 41.16 2.90
145 146 3.628646 ATCGCCAACTCCACCCTGC 62.629 63.158 0.00 0.00 0.00 4.85
146 147 1.746615 CATCGCCAACTCCACCCTG 60.747 63.158 0.00 0.00 0.00 4.45
147 148 1.779061 AACATCGCCAACTCCACCCT 61.779 55.000 0.00 0.00 0.00 4.34
148 149 0.893727 AAACATCGCCAACTCCACCC 60.894 55.000 0.00 0.00 0.00 4.61
149 150 0.521735 GAAACATCGCCAACTCCACC 59.478 55.000 0.00 0.00 0.00 4.61
150 151 0.165944 CGAAACATCGCCAACTCCAC 59.834 55.000 0.00 0.00 0.00 4.02
152 153 1.644786 CCCGAAACATCGCCAACTCC 61.645 60.000 0.00 0.00 0.00 3.85
153 154 1.644786 CCCCGAAACATCGCCAACTC 61.645 60.000 0.00 0.00 0.00 3.01
155 156 1.969589 ACCCCGAAACATCGCCAAC 60.970 57.895 0.00 0.00 0.00 3.77
156 157 1.969064 CACCCCGAAACATCGCCAA 60.969 57.895 0.00 0.00 0.00 4.52
159 160 3.131478 CCCACCCCGAAACATCGC 61.131 66.667 0.00 0.00 0.00 4.58
160 161 2.265467 ATCCCCACCCCGAAACATCG 62.265 60.000 0.00 0.00 0.00 3.84
161 162 0.751643 CATCCCCACCCCGAAACATC 60.752 60.000 0.00 0.00 0.00 3.06
162 163 1.306296 CATCCCCACCCCGAAACAT 59.694 57.895 0.00 0.00 0.00 2.71
163 164 2.760477 CATCCCCACCCCGAAACA 59.240 61.111 0.00 0.00 0.00 2.83
164 165 2.754254 GCATCCCCACCCCGAAAC 60.754 66.667 0.00 0.00 0.00 2.78
176 177 3.880846 CTCCTTTGCGGCGCATCC 61.881 66.667 36.69 5.14 38.76 3.51
177 178 3.880846 CCTCCTTTGCGGCGCATC 61.881 66.667 36.69 5.58 38.76 3.91
185 186 3.373565 CAACCCCGCCTCCTTTGC 61.374 66.667 0.00 0.00 0.00 3.68
186 187 2.676471 CCAACCCCGCCTCCTTTG 60.676 66.667 0.00 0.00 0.00 2.77
187 188 3.979497 CCCAACCCCGCCTCCTTT 61.979 66.667 0.00 0.00 0.00 3.11
197 198 4.506255 CATCGCCTCCCCCAACCC 62.506 72.222 0.00 0.00 0.00 4.11
199 200 4.424711 TGCATCGCCTCCCCCAAC 62.425 66.667 0.00 0.00 0.00 3.77
200 201 4.113815 CTGCATCGCCTCCCCCAA 62.114 66.667 0.00 0.00 0.00 4.12
263 264 4.241555 CCAATCCCGCCTCCTCCG 62.242 72.222 0.00 0.00 0.00 4.63
273 274 3.825623 CTCCTGGCCCCCAATCCC 61.826 72.222 0.00 0.00 30.80 3.85
286 287 1.043673 GTAGATGTGTCGCCCCTCCT 61.044 60.000 0.00 0.00 0.00 3.69
287 288 1.043673 AGTAGATGTGTCGCCCCTCC 61.044 60.000 0.00 0.00 0.00 4.30
288 289 1.337387 GTAGTAGATGTGTCGCCCCTC 59.663 57.143 0.00 0.00 0.00 4.30
289 290 1.400737 GTAGTAGATGTGTCGCCCCT 58.599 55.000 0.00 0.00 0.00 4.79
290 291 0.388294 GGTAGTAGATGTGTCGCCCC 59.612 60.000 0.00 0.00 0.00 5.80
291 292 1.108776 TGGTAGTAGATGTGTCGCCC 58.891 55.000 0.00 0.00 0.00 6.13
292 293 1.749634 AGTGGTAGTAGATGTGTCGCC 59.250 52.381 0.00 0.00 0.00 5.54
293 294 3.376234 TGTAGTGGTAGTAGATGTGTCGC 59.624 47.826 0.00 0.00 0.00 5.19
295 296 6.812160 CCTTTTGTAGTGGTAGTAGATGTGTC 59.188 42.308 0.00 0.00 0.00 3.67
296 297 6.495872 TCCTTTTGTAGTGGTAGTAGATGTGT 59.504 38.462 0.00 0.00 0.00 3.72
297 298 6.931838 TCCTTTTGTAGTGGTAGTAGATGTG 58.068 40.000 0.00 0.00 0.00 3.21
314 315 3.077484 TCTGCCCATCTCTTCCTTTTG 57.923 47.619 0.00 0.00 0.00 2.44
327 328 4.299586 TGTGATTGTTTAGATCTGCCCA 57.700 40.909 5.18 0.00 0.00 5.36
350 351 7.820872 GGGCCATTAGATTTTAATGATGAATGG 59.179 37.037 4.39 11.71 43.19 3.16
361 362 8.511126 AGAAGGATTTAGGGCCATTAGATTTTA 58.489 33.333 6.18 0.00 0.00 1.52
396 397 3.190535 GGCTTAATGTGTGGTTGGTAGTG 59.809 47.826 0.00 0.00 0.00 2.74
398 399 3.190535 GTGGCTTAATGTGTGGTTGGTAG 59.809 47.826 0.00 0.00 0.00 3.18
409 410 2.165641 TCGATCGACTGTGGCTTAATGT 59.834 45.455 15.15 0.00 0.00 2.71
430 431 2.031163 GCGGGGCAGATTAGCGAT 59.969 61.111 0.00 0.00 34.64 4.58
433 434 1.604604 TTAATGCGGGGCAGATTAGC 58.395 50.000 0.00 0.00 43.65 3.09
457 458 0.447011 CGTGCGGGCGGTTTTATTTA 59.553 50.000 0.00 0.00 0.00 1.40
461 462 3.043121 GTCGTGCGGGCGGTTTTA 61.043 61.111 0.00 0.00 0.00 1.52
483 484 0.462759 GAGGTCATGCGGGAGAAAGG 60.463 60.000 0.00 0.00 0.00 3.11
485 486 0.909610 AGGAGGTCATGCGGGAGAAA 60.910 55.000 0.00 0.00 0.00 2.52
488 489 1.144936 GAAGGAGGTCATGCGGGAG 59.855 63.158 0.00 0.00 0.00 4.30
489 490 1.306141 AGAAGGAGGTCATGCGGGA 60.306 57.895 0.00 0.00 0.00 5.14
490 491 1.144936 GAGAAGGAGGTCATGCGGG 59.855 63.158 0.00 0.00 0.00 6.13
491 492 1.144936 GGAGAAGGAGGTCATGCGG 59.855 63.158 0.00 0.00 0.00 5.69
492 493 0.103937 GAGGAGAAGGAGGTCATGCG 59.896 60.000 0.00 0.00 0.00 4.73
493 494 1.412343 GAGAGGAGAAGGAGGTCATGC 59.588 57.143 0.00 0.00 0.00 4.06
494 495 1.680735 CGAGAGGAGAAGGAGGTCATG 59.319 57.143 0.00 0.00 0.00 3.07
495 496 2.026905 GCGAGAGGAGAAGGAGGTCAT 61.027 57.143 0.00 0.00 0.00 3.06
500 501 2.411290 GCGCGAGAGGAGAAGGAG 59.589 66.667 12.10 0.00 0.00 3.69
501 502 3.141488 GGCGCGAGAGGAGAAGGA 61.141 66.667 12.10 0.00 0.00 3.36
502 503 4.560856 CGGCGCGAGAGGAGAAGG 62.561 72.222 12.10 0.00 0.00 3.46
503 504 3.343788 AACGGCGCGAGAGGAGAAG 62.344 63.158 12.10 0.00 0.00 2.85
504 505 3.338126 GAACGGCGCGAGAGGAGAA 62.338 63.158 12.10 0.00 0.00 2.87
505 506 3.812019 GAACGGCGCGAGAGGAGA 61.812 66.667 12.10 0.00 0.00 3.71
560 561 4.052229 ACGACTTCCCGTGGCTCG 62.052 66.667 1.28 1.28 41.70 5.03
600 601 3.059982 CTTCCTGTGGCTCCGACA 58.940 61.111 0.00 0.00 0.00 4.35
602 603 3.706373 GGCTTCCTGTGGCTCCGA 61.706 66.667 0.00 0.00 0.00 4.55
707 708 4.680237 CGGAGGCGGTGAACAGCA 62.680 66.667 7.84 0.00 38.83 4.41
772 795 1.078759 CTTACTTGCGACTCCAGCGG 61.079 60.000 0.00 0.00 37.44 5.52
773 796 1.687494 GCTTACTTGCGACTCCAGCG 61.687 60.000 0.00 0.00 37.44 5.18
775 798 1.996191 GAAGCTTACTTGCGACTCCAG 59.004 52.381 0.00 0.00 35.82 3.86
792 815 7.222417 CAGTGTAGATGAGTTCAGCAATAGAAG 59.778 40.741 0.00 0.00 34.14 2.85
814 837 1.679139 TGGTTTGCTTGGTCTCAGTG 58.321 50.000 0.00 0.00 0.00 3.66
956 991 4.774503 GCCAAGCTGAGCGGCTCT 62.775 66.667 28.42 7.97 42.24 4.09
1077 1112 2.926778 ATAGCAGCACCTCAGATTCC 57.073 50.000 0.00 0.00 0.00 3.01
1128 3022 9.658799 AGACGCGGTATAGAAGTATAAGTATTA 57.341 33.333 12.47 0.00 33.48 0.98
1213 3120 3.809832 CCAGATTATCCAAAATCGTCGCT 59.190 43.478 0.00 0.00 40.19 4.93
1271 3187 2.944349 AGCATTGTTTTTGCCAAACTGG 59.056 40.909 9.37 0.00 41.06 4.00
1283 3199 7.885297 TGCTGAACTTAATCTTAGCATTGTTT 58.115 30.769 0.00 0.00 36.37 2.83
1334 3250 6.814954 ACCATAGTATTTGTGAGAGTGGAT 57.185 37.500 0.00 0.00 0.00 3.41
1353 3278 1.967779 GGGCAAACAACTACCAACCAT 59.032 47.619 0.00 0.00 0.00 3.55
1667 4078 7.211573 TCATCCTTTCGAAGTTGTACTGTAAA 58.788 34.615 0.00 0.00 0.00 2.01
1801 4219 5.420104 AGGAGTTCATGCAGAAATAAAAGGG 59.580 40.000 0.00 0.00 38.13 3.95
1817 4235 5.419155 CAGGAAGTACATACTGAGGAGTTCA 59.581 44.000 4.19 0.00 36.50 3.18
1877 4295 4.154375 TCGACTGTACTTCTGAGTGTGATC 59.846 45.833 0.00 0.00 36.60 2.92
1887 4305 2.729194 AGAGCCATCGACTGTACTTCT 58.271 47.619 0.00 0.00 0.00 2.85
1940 4358 6.236017 TGGTAAGTTTTCATCGTCACATTC 57.764 37.500 0.00 0.00 0.00 2.67
1991 4409 6.542370 GCTTAGCAATTTAGTAGGGATGTCAA 59.458 38.462 0.00 0.00 0.00 3.18
1996 4414 5.625150 CTGGCTTAGCAATTTAGTAGGGAT 58.375 41.667 6.53 0.00 0.00 3.85
1997 4415 5.036117 CTGGCTTAGCAATTTAGTAGGGA 57.964 43.478 6.53 0.00 0.00 4.20
2032 4450 3.862877 AAAGGAAAAAGGCAAGGCAAT 57.137 38.095 0.00 0.00 0.00 3.56
2047 4465 8.095169 GGTTCTTATCAGTACAGAGAAAAAGGA 58.905 37.037 0.00 0.00 0.00 3.36
2055 4473 3.700038 ACCGGGTTCTTATCAGTACAGAG 59.300 47.826 6.32 0.00 0.00 3.35
2057 4475 4.181578 CAACCGGGTTCTTATCAGTACAG 58.818 47.826 10.04 0.00 0.00 2.74
2061 4479 3.782656 AACAACCGGGTTCTTATCAGT 57.217 42.857 10.04 0.00 0.00 3.41
2065 4483 4.077108 GAGGAAAACAACCGGGTTCTTAT 58.923 43.478 10.04 0.00 0.00 1.73
2082 4500 0.984961 CAGGGCCATGAGAGGAGGAA 60.985 60.000 13.35 0.00 0.00 3.36
2088 4506 4.696479 ATACTTAACAGGGCCATGAGAG 57.304 45.455 26.87 19.23 0.00 3.20
2276 5265 0.679640 CTGCCCGGCCAAAGTCATTA 60.680 55.000 7.03 0.00 0.00 1.90
2277 5266 1.978617 CTGCCCGGCCAAAGTCATT 60.979 57.895 7.03 0.00 0.00 2.57
2284 5273 2.124193 CATCATCTGCCCGGCCAA 60.124 61.111 7.03 0.00 0.00 4.52
2285 5274 4.881440 GCATCATCTGCCCGGCCA 62.881 66.667 7.03 0.00 45.66 5.36
2321 5310 1.477295 TGGAGTGTGTGTACGACAACA 59.523 47.619 0.00 0.00 35.91 3.33
2323 5312 2.963548 TTGGAGTGTGTGTACGACAA 57.036 45.000 0.00 0.00 35.91 3.18
2409 5398 6.260714 GCATTTTTGTTCTTTCAACCATCCTT 59.739 34.615 0.00 0.00 0.00 3.36
2539 5529 9.851686 AAATCTCCAATTGCTCACAGTATAATA 57.148 29.630 0.00 0.00 0.00 0.98
2540 5530 8.627403 CAAATCTCCAATTGCTCACAGTATAAT 58.373 33.333 0.00 0.00 0.00 1.28
2541 5531 7.828717 TCAAATCTCCAATTGCTCACAGTATAA 59.171 33.333 0.00 0.00 0.00 0.98
2543 5533 6.094603 GTCAAATCTCCAATTGCTCACAGTAT 59.905 38.462 0.00 0.00 0.00 2.12
2599 5589 3.094484 TCCAGATTTACGCCCCAATTT 57.906 42.857 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.