Multiple sequence alignment - TraesCS5B01G046900

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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 TraesCS5B01G046900 chr5B 100.000 4519 0 0 1 4519 52650794 52646276 0.000000e+00 8346.0
1 TraesCS5B01G046900 chr5B 99.872 3894 5 0 1 3894 52914150 52918043 0.000000e+00 7164.0
2 TraesCS5B01G046900 chr5B 90.909 396 29 7 150 541 57900589 57900197 4.000000e-145 525.0
3 TraesCS5B01G046900 chr5B 77.657 461 64 18 1028 1480 45539559 45539130 1.260000e-60 244.0
4 TraesCS5B01G046900 chr5B 90.503 179 15 2 3909 4085 295174706 295174884 7.560000e-58 235.0
5 TraesCS5B01G046900 chr5B 79.894 189 27 8 2069 2255 45538274 45538095 1.320000e-25 128.0
6 TraesCS5B01G046900 chr5D 97.729 3038 49 4 904 3923 49763963 49760928 0.000000e+00 5210.0
7 TraesCS5B01G046900 chr5D 95.662 3043 73 19 904 3923 50200625 50197619 0.000000e+00 4833.0
8 TraesCS5B01G046900 chr5D 97.316 2720 46 8 1222 3923 50039228 50036518 0.000000e+00 4593.0
9 TraesCS5B01G046900 chr5D 96.487 427 6 5 4097 4519 50197597 50197176 0.000000e+00 697.0
10 TraesCS5B01G046900 chr5D 96.019 427 8 6 4097 4519 50036496 50036075 0.000000e+00 686.0
11 TraesCS5B01G046900 chr5D 94.350 354 7 7 4170 4519 49760855 49760511 8.610000e-147 531.0
12 TraesCS5B01G046900 chr5D 94.040 151 8 1 2 152 49764112 49763963 1.260000e-55 228.0
13 TraesCS5B01G046900 chr5D 94.040 151 8 1 2 152 50200774 50200625 1.260000e-55 228.0
14 TraesCS5B01G046900 chr5D 86.486 185 17 7 4097 4276 171681145 171681326 3.570000e-46 196.0
15 TraesCS5B01G046900 chr5D 100.000 53 0 0 4097 4149 49760906 49760854 1.030000e-16 99.0
16 TraesCS5B01G046900 chr5D 89.231 65 6 1 2126 2189 45487978 45487914 3.750000e-11 80.5
17 TraesCS5B01G046900 chr5A 95.191 3057 76 30 904 3923 39244601 39241579 0.000000e+00 4765.0
18 TraesCS5B01G046900 chr5A 95.785 427 9 5 4097 4519 39241557 39241136 0.000000e+00 680.0
19 TraesCS5B01G046900 chr5A 88.835 206 11 7 4323 4519 708833768 708833566 4.520000e-60 243.0
20 TraesCS5B01G046900 chr5A 87.970 133 12 3 4149 4277 490149654 490149786 2.180000e-33 154.0
21 TraesCS5B01G046900 chr5A 77.990 209 36 7 2069 2275 36365651 36365451 6.140000e-24 122.0
22 TraesCS5B01G046900 chrUn 99.889 1799 2 0 2096 3894 371433358 371431560 0.000000e+00 3312.0
23 TraesCS5B01G046900 chrUn 97.923 915 16 1 918 1829 460220116 460221030 0.000000e+00 1581.0
24 TraesCS5B01G046900 chrUn 88.512 383 33 2 541 912 195342819 195343201 1.920000e-123 453.0
25 TraesCS5B01G046900 chrUn 88.512 383 33 4 541 912 350819886 350819504 1.920000e-123 453.0
26 TraesCS5B01G046900 chrUn 88.512 383 33 2 541 912 350842606 350842224 1.920000e-123 453.0
27 TraesCS5B01G046900 chrUn 88.512 383 33 2 541 912 404005934 404006316 1.920000e-123 453.0
28 TraesCS5B01G046900 chr7B 98.808 755 9 0 150 904 515969502 515970256 0.000000e+00 1345.0
29 TraesCS5B01G046900 chr7B 92.814 167 12 0 3920 4086 423756647 423756481 4.520000e-60 243.0
30 TraesCS5B01G046900 chr7B 92.683 164 12 0 3922 4085 411788252 411788415 2.100000e-58 237.0
31 TraesCS5B01G046900 chr1D 92.010 388 25 5 158 542 30366000 30366384 1.430000e-149 540.0
32 TraesCS5B01G046900 chr1D 88.802 384 30 4 541 913 58119489 58119870 4.120000e-125 459.0
33 TraesCS5B01G046900 chr3B 91.139 395 28 7 151 541 230489680 230489289 3.100000e-146 529.0
34 TraesCS5B01G046900 chr3B 92.899 169 12 0 3918 4086 52744110 52743942 3.490000e-61 246.0
35 TraesCS5B01G046900 chr3B 88.557 201 16 3 4323 4519 458277286 458277089 2.100000e-58 237.0
36 TraesCS5B01G046900 chr3B 88.636 132 9 4 4149 4277 458277560 458277432 6.050000e-34 156.0
37 TraesCS5B01G046900 chr6B 91.071 392 28 7 154 541 221411555 221411167 1.440000e-144 523.0
38 TraesCS5B01G046900 chr6B 90.588 85 7 1 2937 3020 172738845 172738929 1.330000e-20 111.0
39 TraesCS5B01G046900 chr1A 89.899 396 35 5 151 543 79830557 79830950 5.220000e-139 505.0
40 TraesCS5B01G046900 chr1A 94.406 143 6 2 3187 3328 547018797 547018656 7.610000e-53 219.0
41 TraesCS5B01G046900 chr1A 94.928 138 6 1 3189 3326 388684886 388685022 9.850000e-52 215.0
42 TraesCS5B01G046900 chr6D 91.176 374 23 4 541 904 6843382 6843009 2.430000e-137 499.0
43 TraesCS5B01G046900 chr6D 88.571 210 16 4 4314 4519 14025586 14025791 9.710000e-62 248.0
44 TraesCS5B01G046900 chr6D 87.500 184 13 8 4102 4279 14025293 14025472 2.130000e-48 204.0
45 TraesCS5B01G046900 chr6D 91.765 85 6 1 2937 3020 90111901 90111817 2.860000e-22 117.0
46 TraesCS5B01G046900 chr2D 89.390 377 30 4 541 907 66439691 66440067 2.460000e-127 466.0
47 TraesCS5B01G046900 chr2D 91.477 176 11 4 3922 4095 603086718 603086891 5.840000e-59 239.0
48 TraesCS5B01G046900 chr2D 92.222 90 5 1 152 241 606423116 606423203 4.750000e-25 126.0
49 TraesCS5B01G046900 chr2D 90.805 87 4 3 2936 3020 425742653 425742569 3.690000e-21 113.0
50 TraesCS5B01G046900 chr7A 88.095 336 27 3 586 911 496835671 496836003 1.970000e-103 387.0
51 TraesCS5B01G046900 chr7A 86.893 206 15 3 541 734 664539679 664539474 2.120000e-53 220.0
52 TraesCS5B01G046900 chr7A 86.861 137 14 3 4145 4277 454755053 454755189 2.820000e-32 150.0
53 TraesCS5B01G046900 chr6A 89.524 210 15 3 4314 4519 15380598 15380804 4.480000e-65 259.0
54 TraesCS5B01G046900 chr6A 90.816 98 5 3 4097 4192 15379815 15379910 1.320000e-25 128.0
55 TraesCS5B01G046900 chr4A 89.552 201 14 4 4323 4519 261150493 261150690 9.710000e-62 248.0
56 TraesCS5B01G046900 chr4A 92.857 168 12 0 3919 4086 713022018 713022185 1.260000e-60 244.0
57 TraesCS5B01G046900 chr1B 91.713 181 12 3 150 328 613737452 613737631 9.710000e-62 248.0
58 TraesCS5B01G046900 chr3D 92.353 170 12 1 3917 4086 604896779 604896947 1.620000e-59 241.0
59 TraesCS5B01G046900 chr3D 91.429 175 13 2 3922 4095 357946562 357946735 5.840000e-59 239.0
60 TraesCS5B01G046900 chr4B 90.055 181 16 2 3910 4090 338425957 338425779 2.720000e-57 233.0
61 TraesCS5B01G046900 chr4B 93.151 146 6 3 3190 3332 13408963 13409107 1.270000e-50 211.0
62 TraesCS5B01G046900 chr2A 86.408 206 17 2 532 726 278925512 278925717 9.850000e-52 215.0


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 TraesCS5B01G046900 chr5B 52646276 52650794 4518 True 8346.000000 8346 100.000000 1 4519 1 chr5B.!!$R1 4518
1 TraesCS5B01G046900 chr5B 52914150 52918043 3893 False 7164.000000 7164 99.872000 1 3894 1 chr5B.!!$F1 3893
2 TraesCS5B01G046900 chr5D 50036075 50039228 3153 True 2639.500000 4593 96.667500 1222 4519 2 chr5D.!!$R3 3297
3 TraesCS5B01G046900 chr5D 50197176 50200774 3598 True 1919.333333 4833 95.396333 2 4519 3 chr5D.!!$R4 4517
4 TraesCS5B01G046900 chr5D 49760511 49764112 3601 True 1517.000000 5210 96.529750 2 4519 4 chr5D.!!$R2 4517
5 TraesCS5B01G046900 chr5A 39241136 39244601 3465 True 2722.500000 4765 95.488000 904 4519 2 chr5A.!!$R3 3615
6 TraesCS5B01G046900 chrUn 371431560 371433358 1798 True 3312.000000 3312 99.889000 2096 3894 1 chrUn.!!$R3 1798
7 TraesCS5B01G046900 chrUn 460220116 460221030 914 False 1581.000000 1581 97.923000 918 1829 1 chrUn.!!$F3 911
8 TraesCS5B01G046900 chr7B 515969502 515970256 754 False 1345.000000 1345 98.808000 150 904 1 chr7B.!!$F2 754

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
645 646 1.079127 AACGCATCTGGGGACGAAG 60.079 57.895 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3923 4189 8.581253 AGACAAATATTTAGGAACAAAGGGAG 57.419 34.615 0.0 0.0 0.0 4.3 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
645 646 1.079127 AACGCATCTGGGGACGAAG 60.079 57.895 0.00 0.00 0.00 3.79
3923 4189 5.806502 GTGTTGGGGTGTTTTTGTTTACTAC 59.193 40.000 0.00 0.00 0.00 2.73
3924 4190 5.715753 TGTTGGGGTGTTTTTGTTTACTACT 59.284 36.000 0.00 0.00 0.00 2.57
3925 4191 6.127675 TGTTGGGGTGTTTTTGTTTACTACTC 60.128 38.462 0.00 0.00 0.00 2.59
3926 4192 4.888823 TGGGGTGTTTTTGTTTACTACTCC 59.111 41.667 0.00 0.00 0.00 3.85
3927 4193 4.279169 GGGGTGTTTTTGTTTACTACTCCC 59.721 45.833 0.00 0.00 40.24 4.30
3928 4194 5.135383 GGGTGTTTTTGTTTACTACTCCCT 58.865 41.667 0.00 0.00 38.73 4.20
3929 4195 5.595542 GGGTGTTTTTGTTTACTACTCCCTT 59.404 40.000 0.00 0.00 38.73 3.95
3930 4196 6.097270 GGGTGTTTTTGTTTACTACTCCCTTT 59.903 38.462 0.00 0.00 38.73 3.11
3931 4197 6.976349 GGTGTTTTTGTTTACTACTCCCTTTG 59.024 38.462 0.00 0.00 0.00 2.77
3932 4198 7.363181 GGTGTTTTTGTTTACTACTCCCTTTGT 60.363 37.037 0.00 0.00 0.00 2.83
3933 4199 8.030692 GTGTTTTTGTTTACTACTCCCTTTGTT 58.969 33.333 0.00 0.00 0.00 2.83
3934 4200 8.245491 TGTTTTTGTTTACTACTCCCTTTGTTC 58.755 33.333 0.00 0.00 0.00 3.18
3935 4201 6.947644 TTTGTTTACTACTCCCTTTGTTCC 57.052 37.500 0.00 0.00 0.00 3.62
3936 4202 5.899631 TGTTTACTACTCCCTTTGTTCCT 57.100 39.130 0.00 0.00 0.00 3.36
3937 4203 6.999705 TGTTTACTACTCCCTTTGTTCCTA 57.000 37.500 0.00 0.00 0.00 2.94
3938 4204 7.377696 TGTTTACTACTCCCTTTGTTCCTAA 57.622 36.000 0.00 0.00 0.00 2.69
3939 4205 7.804147 TGTTTACTACTCCCTTTGTTCCTAAA 58.196 34.615 0.00 0.00 0.00 1.85
3940 4206 8.442374 TGTTTACTACTCCCTTTGTTCCTAAAT 58.558 33.333 0.00 0.00 0.00 1.40
3941 4207 9.948964 GTTTACTACTCCCTTTGTTCCTAAATA 57.051 33.333 0.00 0.00 0.00 1.40
3945 4211 9.462606 ACTACTCCCTTTGTTCCTAAATATTTG 57.537 33.333 11.05 1.40 0.00 2.32
3946 4212 9.462606 CTACTCCCTTTGTTCCTAAATATTTGT 57.537 33.333 11.05 0.00 0.00 2.83
3947 4213 8.349568 ACTCCCTTTGTTCCTAAATATTTGTC 57.650 34.615 11.05 0.00 0.00 3.18
3948 4214 8.170730 ACTCCCTTTGTTCCTAAATATTTGTCT 58.829 33.333 11.05 0.00 0.00 3.41
3949 4215 8.950007 TCCCTTTGTTCCTAAATATTTGTCTT 57.050 30.769 11.05 0.00 0.00 3.01
3950 4216 9.374711 TCCCTTTGTTCCTAAATATTTGTCTTT 57.625 29.630 11.05 0.00 0.00 2.52
3951 4217 9.639601 CCCTTTGTTCCTAAATATTTGTCTTTC 57.360 33.333 11.05 0.00 0.00 2.62
3966 4232 8.924511 ATTTGTCTTTCTAGAGATTTCACCAA 57.075 30.769 0.00 0.00 0.00 3.67
3967 4233 7.969536 TTGTCTTTCTAGAGATTTCACCAAG 57.030 36.000 0.00 0.00 0.00 3.61
3968 4234 7.067496 TGTCTTTCTAGAGATTTCACCAAGT 57.933 36.000 0.00 0.00 0.00 3.16
3969 4235 6.931281 TGTCTTTCTAGAGATTTCACCAAGTG 59.069 38.462 0.00 0.00 34.45 3.16
3970 4236 7.155328 GTCTTTCTAGAGATTTCACCAAGTGA 58.845 38.462 0.00 0.00 41.09 3.41
3971 4237 7.117092 GTCTTTCTAGAGATTTCACCAAGTGAC 59.883 40.741 0.00 0.00 42.60 3.67
3972 4238 6.672266 TTCTAGAGATTTCACCAAGTGACT 57.328 37.500 0.00 0.00 42.60 3.41
3973 4239 7.776618 TTCTAGAGATTTCACCAAGTGACTA 57.223 36.000 0.00 0.00 42.60 2.59
3974 4240 7.159322 TCTAGAGATTTCACCAAGTGACTAC 57.841 40.000 0.00 0.00 42.60 2.73
3975 4241 5.808366 AGAGATTTCACCAAGTGACTACA 57.192 39.130 0.00 0.00 42.60 2.74
3976 4242 6.365970 AGAGATTTCACCAAGTGACTACAT 57.634 37.500 0.00 0.00 42.60 2.29
3977 4243 7.482169 AGAGATTTCACCAAGTGACTACATA 57.518 36.000 0.00 0.00 42.60 2.29
3978 4244 8.083828 AGAGATTTCACCAAGTGACTACATAT 57.916 34.615 0.00 0.00 42.60 1.78
3979 4245 7.984050 AGAGATTTCACCAAGTGACTACATATG 59.016 37.037 0.00 0.00 42.60 1.78
3980 4246 7.851228 AGATTTCACCAAGTGACTACATATGA 58.149 34.615 10.38 0.00 42.60 2.15
3981 4247 8.321353 AGATTTCACCAAGTGACTACATATGAA 58.679 33.333 10.38 0.00 42.60 2.57
3982 4248 7.905604 TTTCACCAAGTGACTACATATGAAG 57.094 36.000 10.38 0.00 42.60 3.02
3983 4249 5.419542 TCACCAAGTGACTACATATGAAGC 58.580 41.667 10.38 0.00 37.67 3.86
3984 4250 5.046663 TCACCAAGTGACTACATATGAAGCA 60.047 40.000 10.38 0.00 37.67 3.91
3985 4251 5.643348 CACCAAGTGACTACATATGAAGCAA 59.357 40.000 10.38 0.00 35.23 3.91
3986 4252 6.149308 CACCAAGTGACTACATATGAAGCAAA 59.851 38.462 10.38 0.00 35.23 3.68
3987 4253 6.714810 ACCAAGTGACTACATATGAAGCAAAA 59.285 34.615 10.38 0.00 0.00 2.44
3988 4254 7.394359 ACCAAGTGACTACATATGAAGCAAAAT 59.606 33.333 10.38 0.00 0.00 1.82
3989 4255 8.892723 CCAAGTGACTACATATGAAGCAAAATA 58.107 33.333 10.38 0.00 0.00 1.40
3992 4258 9.672673 AGTGACTACATATGAAGCAAAATAAGT 57.327 29.630 10.38 0.00 0.00 2.24
3993 4259 9.708222 GTGACTACATATGAAGCAAAATAAGTG 57.292 33.333 10.38 0.00 0.00 3.16
3994 4260 9.665719 TGACTACATATGAAGCAAAATAAGTGA 57.334 29.630 10.38 0.00 0.00 3.41
4003 4269 8.284945 TGAAGCAAAATAAGTGAATCTATGCT 57.715 30.769 0.00 0.00 42.88 3.79
4004 4270 8.400947 TGAAGCAAAATAAGTGAATCTATGCTC 58.599 33.333 0.00 0.00 40.42 4.26
4005 4271 8.517062 AAGCAAAATAAGTGAATCTATGCTCT 57.483 30.769 0.00 0.00 40.42 4.09
4006 4272 9.618890 AAGCAAAATAAGTGAATCTATGCTCTA 57.381 29.630 0.00 0.00 40.42 2.43
4007 4273 9.618890 AGCAAAATAAGTGAATCTATGCTCTAA 57.381 29.630 0.00 0.00 37.00 2.10
4038 4304 9.673454 TGTCTATATACATTCGTATGTTGTGTC 57.327 33.333 13.12 0.66 42.29 3.67
4039 4305 9.125906 GTCTATATACATTCGTATGTTGTGTCC 57.874 37.037 13.12 0.00 42.29 4.02
4040 4306 8.852135 TCTATATACATTCGTATGTTGTGTCCA 58.148 33.333 13.12 0.00 42.29 4.02
4041 4307 9.639601 CTATATACATTCGTATGTTGTGTCCAT 57.360 33.333 13.12 1.80 42.29 3.41
4042 4308 8.902540 ATATACATTCGTATGTTGTGTCCATT 57.097 30.769 13.12 0.00 42.29 3.16
4043 4309 5.957842 ACATTCGTATGTTGTGTCCATTT 57.042 34.783 1.31 0.00 42.29 2.32
4044 4310 5.698832 ACATTCGTATGTTGTGTCCATTTG 58.301 37.500 1.31 0.00 42.29 2.32
4045 4311 5.471797 ACATTCGTATGTTGTGTCCATTTGA 59.528 36.000 1.31 0.00 42.29 2.69
4046 4312 6.016693 ACATTCGTATGTTGTGTCCATTTGAA 60.017 34.615 1.31 0.00 42.29 2.69
4047 4313 6.378710 TTCGTATGTTGTGTCCATTTGAAA 57.621 33.333 0.00 0.00 0.00 2.69
4048 4314 6.567687 TCGTATGTTGTGTCCATTTGAAAT 57.432 33.333 0.00 0.00 0.00 2.17
4049 4315 6.377780 TCGTATGTTGTGTCCATTTGAAATG 58.622 36.000 10.84 10.84 0.00 2.32
4050 4316 5.060816 CGTATGTTGTGTCCATTTGAAATGC 59.939 40.000 12.26 0.87 0.00 3.56
4051 4317 3.726607 TGTTGTGTCCATTTGAAATGCC 58.273 40.909 12.26 5.75 0.00 4.40
4052 4318 3.387374 TGTTGTGTCCATTTGAAATGCCT 59.613 39.130 12.26 0.00 0.00 4.75
4053 4319 4.586421 TGTTGTGTCCATTTGAAATGCCTA 59.414 37.500 12.26 0.00 0.00 3.93
4054 4320 5.163513 GTTGTGTCCATTTGAAATGCCTAG 58.836 41.667 12.26 0.00 0.00 3.02
4055 4321 4.661222 TGTGTCCATTTGAAATGCCTAGA 58.339 39.130 12.26 1.83 0.00 2.43
4056 4322 5.076182 TGTGTCCATTTGAAATGCCTAGAA 58.924 37.500 12.26 0.00 0.00 2.10
4057 4323 5.538053 TGTGTCCATTTGAAATGCCTAGAAA 59.462 36.000 12.26 0.00 0.00 2.52
4058 4324 6.095377 GTGTCCATTTGAAATGCCTAGAAAG 58.905 40.000 12.26 0.00 0.00 2.62
4059 4325 6.009589 TGTCCATTTGAAATGCCTAGAAAGA 58.990 36.000 12.26 0.00 0.00 2.52
4060 4326 6.071952 TGTCCATTTGAAATGCCTAGAAAGAC 60.072 38.462 12.26 11.27 0.00 3.01
4061 4327 6.009589 TCCATTTGAAATGCCTAGAAAGACA 58.990 36.000 12.26 0.00 0.00 3.41
4062 4328 6.493115 TCCATTTGAAATGCCTAGAAAGACAA 59.507 34.615 12.26 0.00 0.00 3.18
4063 4329 7.015098 TCCATTTGAAATGCCTAGAAAGACAAA 59.985 33.333 12.26 0.00 0.00 2.83
4064 4330 7.820872 CCATTTGAAATGCCTAGAAAGACAAAT 59.179 33.333 12.26 0.00 36.38 2.32
4065 4331 9.859427 CATTTGAAATGCCTAGAAAGACAAATA 57.141 29.630 4.82 0.00 34.96 1.40
4069 4335 9.859427 TGAAATGCCTAGAAAGACAAATATTTG 57.141 29.630 23.60 23.60 43.62 2.32
4070 4336 9.305925 GAAATGCCTAGAAAGACAAATATTTGG 57.694 33.333 27.43 12.85 42.34 3.28
4071 4337 8.593945 AATGCCTAGAAAGACAAATATTTGGA 57.406 30.769 27.43 2.86 42.34 3.53
4072 4338 8.593945 ATGCCTAGAAAGACAAATATTTGGAA 57.406 30.769 27.43 5.94 42.34 3.53
4073 4339 8.415950 TGCCTAGAAAGACAAATATTTGGAAA 57.584 30.769 27.43 8.61 42.34 3.13
4074 4340 8.303876 TGCCTAGAAAGACAAATATTTGGAAAC 58.696 33.333 27.43 16.80 42.34 2.78
4075 4341 7.484959 GCCTAGAAAGACAAATATTTGGAAACG 59.515 37.037 27.43 6.31 42.34 3.60
4076 4342 7.968405 CCTAGAAAGACAAATATTTGGAAACGG 59.032 37.037 27.43 14.87 42.34 4.44
4077 4343 7.519032 AGAAAGACAAATATTTGGAAACGGA 57.481 32.000 27.43 0.00 42.34 4.69
4078 4344 7.593825 AGAAAGACAAATATTTGGAAACGGAG 58.406 34.615 27.43 4.34 42.34 4.63
4079 4345 5.897377 AGACAAATATTTGGAAACGGAGG 57.103 39.130 27.43 3.68 42.34 4.30
4080 4346 4.705023 AGACAAATATTTGGAAACGGAGGG 59.295 41.667 27.43 3.22 42.34 4.30
4081 4347 4.668636 ACAAATATTTGGAAACGGAGGGA 58.331 39.130 27.43 0.00 42.34 4.20
4082 4348 4.705023 ACAAATATTTGGAAACGGAGGGAG 59.295 41.667 27.43 2.64 42.34 4.30
4083 4349 4.586306 AATATTTGGAAACGGAGGGAGT 57.414 40.909 0.00 0.00 0.00 3.85
4084 4350 5.703730 AATATTTGGAAACGGAGGGAGTA 57.296 39.130 0.00 0.00 0.00 2.59
4217 4493 3.119245 TGCTACCAAGATTCGTCACTACC 60.119 47.826 0.00 0.00 0.00 3.18
4254 4530 4.415596 TCCAATTCAACCTAGGCACATTT 58.584 39.130 9.30 0.00 0.00 2.32
4286 4562 9.415544 GCTTAACTCACATTTTCTGAATTCAAT 57.584 29.630 9.88 0.00 0.00 2.57
4298 4576 3.881688 CTGAATTCAATCGGCTTCCTCAT 59.118 43.478 9.88 0.00 0.00 2.90
4410 4690 1.002857 CCCCTTCCTCTTTCCACCAT 58.997 55.000 0.00 0.00 0.00 3.55
4411 4691 1.359130 CCCCTTCCTCTTTCCACCATT 59.641 52.381 0.00 0.00 0.00 3.16
4412 4692 2.225369 CCCCTTCCTCTTTCCACCATTT 60.225 50.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
645 646 2.541556 GTGAGGAGAGATTTACGTGGC 58.458 52.381 0.00 0.00 0.00 5.01
840 841 3.992999 TGTATCCATCAAAAGGCCCAAT 58.007 40.909 0.00 0.00 0.00 3.16
3923 4189 8.581253 AGACAAATATTTAGGAACAAAGGGAG 57.419 34.615 0.00 0.00 0.00 4.30
3924 4190 8.950007 AAGACAAATATTTAGGAACAAAGGGA 57.050 30.769 0.00 0.00 0.00 4.20
3925 4191 9.639601 GAAAGACAAATATTTAGGAACAAAGGG 57.360 33.333 0.00 0.00 0.00 3.95
3941 4207 8.924511 TTGGTGAAATCTCTAGAAAGACAAAT 57.075 30.769 0.00 0.00 0.00 2.32
3942 4208 7.993183 ACTTGGTGAAATCTCTAGAAAGACAAA 59.007 33.333 0.00 0.00 0.00 2.83
3943 4209 7.442364 CACTTGGTGAAATCTCTAGAAAGACAA 59.558 37.037 0.00 0.00 35.23 3.18
3944 4210 6.931281 CACTTGGTGAAATCTCTAGAAAGACA 59.069 38.462 0.00 0.00 35.23 3.41
3945 4211 7.117092 GTCACTTGGTGAAATCTCTAGAAAGAC 59.883 40.741 1.77 0.00 44.49 3.01
3946 4212 7.015682 AGTCACTTGGTGAAATCTCTAGAAAGA 59.984 37.037 1.77 0.00 44.49 2.52
3947 4213 7.158021 AGTCACTTGGTGAAATCTCTAGAAAG 58.842 38.462 1.77 0.00 44.49 2.62
3948 4214 7.067496 AGTCACTTGGTGAAATCTCTAGAAA 57.933 36.000 1.77 0.00 44.49 2.52
3949 4215 6.672266 AGTCACTTGGTGAAATCTCTAGAA 57.328 37.500 1.77 0.00 44.49 2.10
3950 4216 6.719829 TGTAGTCACTTGGTGAAATCTCTAGA 59.280 38.462 1.77 0.00 44.49 2.43
3951 4217 6.925211 TGTAGTCACTTGGTGAAATCTCTAG 58.075 40.000 1.77 0.00 44.49 2.43
3952 4218 6.911250 TGTAGTCACTTGGTGAAATCTCTA 57.089 37.500 1.77 0.00 44.49 2.43
3953 4219 5.808366 TGTAGTCACTTGGTGAAATCTCT 57.192 39.130 1.77 0.00 44.49 3.10
3954 4220 7.981789 TCATATGTAGTCACTTGGTGAAATCTC 59.018 37.037 1.90 0.00 44.49 2.75
3955 4221 7.851228 TCATATGTAGTCACTTGGTGAAATCT 58.149 34.615 1.90 0.00 44.49 2.40
3956 4222 8.492673 TTCATATGTAGTCACTTGGTGAAATC 57.507 34.615 1.90 0.00 44.49 2.17
3957 4223 7.066284 GCTTCATATGTAGTCACTTGGTGAAAT 59.934 37.037 10.61 0.00 44.49 2.17
3958 4224 6.371548 GCTTCATATGTAGTCACTTGGTGAAA 59.628 38.462 10.61 0.00 44.49 2.69
3959 4225 5.874810 GCTTCATATGTAGTCACTTGGTGAA 59.125 40.000 10.61 0.00 44.49 3.18
3960 4226 5.046663 TGCTTCATATGTAGTCACTTGGTGA 60.047 40.000 10.61 0.00 40.50 4.02
3961 4227 5.178061 TGCTTCATATGTAGTCACTTGGTG 58.822 41.667 10.61 0.00 34.45 4.17
3962 4228 5.420725 TGCTTCATATGTAGTCACTTGGT 57.579 39.130 10.61 0.00 0.00 3.67
3963 4229 6.741992 TTTGCTTCATATGTAGTCACTTGG 57.258 37.500 10.61 0.00 0.00 3.61
3966 4232 9.672673 ACTTATTTTGCTTCATATGTAGTCACT 57.327 29.630 10.61 0.00 0.00 3.41
3967 4233 9.708222 CACTTATTTTGCTTCATATGTAGTCAC 57.292 33.333 10.61 0.00 0.00 3.67
3968 4234 9.665719 TCACTTATTTTGCTTCATATGTAGTCA 57.334 29.630 10.61 6.75 0.00 3.41
3977 4243 8.910944 AGCATAGATTCACTTATTTTGCTTCAT 58.089 29.630 0.00 0.00 34.47 2.57
3978 4244 8.284945 AGCATAGATTCACTTATTTTGCTTCA 57.715 30.769 0.00 0.00 34.47 3.02
3979 4245 8.619546 AGAGCATAGATTCACTTATTTTGCTTC 58.380 33.333 0.00 0.00 37.98 3.86
3980 4246 8.517062 AGAGCATAGATTCACTTATTTTGCTT 57.483 30.769 0.00 0.00 37.98 3.91
3981 4247 9.618890 TTAGAGCATAGATTCACTTATTTTGCT 57.381 29.630 0.00 0.00 40.35 3.91
4012 4278 9.673454 GACACAACATACGAATGTATATAGACA 57.327 33.333 2.07 2.07 45.79 3.41
4013 4279 9.125906 GGACACAACATACGAATGTATATAGAC 57.874 37.037 0.00 0.00 45.79 2.59
4014 4280 8.852135 TGGACACAACATACGAATGTATATAGA 58.148 33.333 0.00 0.00 45.79 1.98
4015 4281 9.639601 ATGGACACAACATACGAATGTATATAG 57.360 33.333 0.00 0.00 45.79 1.31
4016 4282 9.990360 AATGGACACAACATACGAATGTATATA 57.010 29.630 0.00 0.00 45.79 0.86
4017 4283 8.902540 AATGGACACAACATACGAATGTATAT 57.097 30.769 0.00 0.00 45.79 0.86
4018 4284 8.608317 CAAATGGACACAACATACGAATGTATA 58.392 33.333 0.00 0.00 45.79 1.47
4019 4285 7.335673 TCAAATGGACACAACATACGAATGTAT 59.664 33.333 0.00 0.00 45.79 2.29
4020 4286 6.651225 TCAAATGGACACAACATACGAATGTA 59.349 34.615 0.00 0.00 45.79 2.29
4022 4288 5.937187 TCAAATGGACACAACATACGAATG 58.063 37.500 0.00 0.00 39.17 2.67
4023 4289 6.567687 TTCAAATGGACACAACATACGAAT 57.432 33.333 0.00 0.00 0.00 3.34
4024 4290 6.378710 TTTCAAATGGACACAACATACGAA 57.621 33.333 0.00 0.00 0.00 3.85
4025 4291 6.377780 CATTTCAAATGGACACAACATACGA 58.622 36.000 1.73 0.00 0.00 3.43
4026 4292 5.060816 GCATTTCAAATGGACACAACATACG 59.939 40.000 12.14 0.00 0.00 3.06
4027 4293 5.348451 GGCATTTCAAATGGACACAACATAC 59.652 40.000 12.14 0.00 0.00 2.39
4028 4294 5.245751 AGGCATTTCAAATGGACACAACATA 59.754 36.000 12.14 0.00 0.00 2.29
4029 4295 4.040706 AGGCATTTCAAATGGACACAACAT 59.959 37.500 12.14 0.00 0.00 2.71
4030 4296 3.387374 AGGCATTTCAAATGGACACAACA 59.613 39.130 12.14 0.00 0.00 3.33
4031 4297 3.993920 AGGCATTTCAAATGGACACAAC 58.006 40.909 12.14 0.00 0.00 3.32
4032 4298 5.076182 TCTAGGCATTTCAAATGGACACAA 58.924 37.500 12.14 0.00 0.00 3.33
4033 4299 4.661222 TCTAGGCATTTCAAATGGACACA 58.339 39.130 12.14 0.00 0.00 3.72
4034 4300 5.643379 TTCTAGGCATTTCAAATGGACAC 57.357 39.130 12.14 0.00 0.00 3.67
4035 4301 6.009589 TCTTTCTAGGCATTTCAAATGGACA 58.990 36.000 12.14 0.00 0.00 4.02
4036 4302 6.071952 TGTCTTTCTAGGCATTTCAAATGGAC 60.072 38.462 12.14 8.23 29.10 4.02
4037 4303 6.009589 TGTCTTTCTAGGCATTTCAAATGGA 58.990 36.000 12.14 0.00 29.10 3.41
4038 4304 6.271488 TGTCTTTCTAGGCATTTCAAATGG 57.729 37.500 12.14 0.00 29.10 3.16
4039 4305 8.767478 ATTTGTCTTTCTAGGCATTTCAAATG 57.233 30.769 5.68 5.68 35.56 2.32
4043 4309 9.859427 CAAATATTTGTCTTTCTAGGCATTTCA 57.141 29.630 18.32 0.00 35.56 2.69
4044 4310 9.305925 CCAAATATTTGTCTTTCTAGGCATTTC 57.694 33.333 23.24 0.00 35.56 2.17
4045 4311 9.034800 TCCAAATATTTGTCTTTCTAGGCATTT 57.965 29.630 23.24 0.00 35.56 2.32
4046 4312 8.593945 TCCAAATATTTGTCTTTCTAGGCATT 57.406 30.769 23.24 0.00 35.56 3.56
4047 4313 8.593945 TTCCAAATATTTGTCTTTCTAGGCAT 57.406 30.769 23.24 0.00 35.56 4.40
4048 4314 8.303876 GTTTCCAAATATTTGTCTTTCTAGGCA 58.696 33.333 23.24 0.00 36.45 4.75
4049 4315 7.484959 CGTTTCCAAATATTTGTCTTTCTAGGC 59.515 37.037 23.24 5.12 36.45 3.93
4050 4316 7.968405 CCGTTTCCAAATATTTGTCTTTCTAGG 59.032 37.037 23.24 13.30 36.45 3.02
4051 4317 8.726988 TCCGTTTCCAAATATTTGTCTTTCTAG 58.273 33.333 23.24 8.49 36.45 2.43
4052 4318 8.624367 TCCGTTTCCAAATATTTGTCTTTCTA 57.376 30.769 23.24 5.03 36.45 2.10
4053 4319 7.309194 CCTCCGTTTCCAAATATTTGTCTTTCT 60.309 37.037 23.24 0.00 36.45 2.52
4054 4320 6.806739 CCTCCGTTTCCAAATATTTGTCTTTC 59.193 38.462 23.24 10.84 36.45 2.62
4055 4321 6.295067 CCCTCCGTTTCCAAATATTTGTCTTT 60.295 38.462 23.24 0.00 36.45 2.52
4056 4322 5.185056 CCCTCCGTTTCCAAATATTTGTCTT 59.815 40.000 23.24 0.00 36.45 3.01
4057 4323 4.705023 CCCTCCGTTTCCAAATATTTGTCT 59.295 41.667 23.24 0.00 36.45 3.41
4058 4324 4.703093 TCCCTCCGTTTCCAAATATTTGTC 59.297 41.667 23.24 11.68 36.45 3.18
4059 4325 4.668636 TCCCTCCGTTTCCAAATATTTGT 58.331 39.130 23.24 0.00 36.45 2.83
4060 4326 4.705023 ACTCCCTCCGTTTCCAAATATTTG 59.295 41.667 19.40 19.40 37.90 2.32
4061 4327 4.930696 ACTCCCTCCGTTTCCAAATATTT 58.069 39.130 0.00 0.00 0.00 1.40
4062 4328 4.586306 ACTCCCTCCGTTTCCAAATATT 57.414 40.909 0.00 0.00 0.00 1.28
4063 4329 4.444449 GCTACTCCCTCCGTTTCCAAATAT 60.444 45.833 0.00 0.00 0.00 1.28
4064 4330 3.118519 GCTACTCCCTCCGTTTCCAAATA 60.119 47.826 0.00 0.00 0.00 1.40
4065 4331 2.355818 GCTACTCCCTCCGTTTCCAAAT 60.356 50.000 0.00 0.00 0.00 2.32
4066 4332 1.002773 GCTACTCCCTCCGTTTCCAAA 59.997 52.381 0.00 0.00 0.00 3.28
4067 4333 0.611714 GCTACTCCCTCCGTTTCCAA 59.388 55.000 0.00 0.00 0.00 3.53
4068 4334 0.543410 TGCTACTCCCTCCGTTTCCA 60.543 55.000 0.00 0.00 0.00 3.53
4069 4335 0.611714 TTGCTACTCCCTCCGTTTCC 59.388 55.000 0.00 0.00 0.00 3.13
4070 4336 2.467566 TTTGCTACTCCCTCCGTTTC 57.532 50.000 0.00 0.00 0.00 2.78
4071 4337 4.451900 CATATTTGCTACTCCCTCCGTTT 58.548 43.478 0.00 0.00 0.00 3.60
4072 4338 3.744530 GCATATTTGCTACTCCCTCCGTT 60.745 47.826 0.35 0.00 45.77 4.44
4073 4339 2.224305 GCATATTTGCTACTCCCTCCGT 60.224 50.000 0.35 0.00 45.77 4.69
4074 4340 2.417719 GCATATTTGCTACTCCCTCCG 58.582 52.381 0.35 0.00 45.77 4.63
4217 4493 7.041848 GGTTGAATTGGAAAATGAGAAAGTTGG 60.042 37.037 0.00 0.00 0.00 3.77
4254 4530 5.177511 CAGAAAATGTGAGTTAAGCGAGTCA 59.822 40.000 0.00 0.00 0.00 3.41
4286 4562 1.982660 AGTCGATATGAGGAAGCCGA 58.017 50.000 0.00 0.00 0.00 5.54
4315 4593 3.126343 GTGGCCCAAAATAGTTCTACGTG 59.874 47.826 0.00 0.00 0.00 4.49
4316 4594 3.008704 AGTGGCCCAAAATAGTTCTACGT 59.991 43.478 0.00 0.00 0.00 3.57
4317 4595 3.606687 AGTGGCCCAAAATAGTTCTACG 58.393 45.455 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.