Multiple sequence alignment - TraesCS5D01G148600

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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 TraesCS5D01G148600 chr5D 100.000 5335 0 0 1 5335 236665394 236660060 0.000000e+00 9852
1 TraesCS5D01G148600 chr5B 92.235 5048 182 78 1 4944 268429845 268434786 0.000000e+00 6957
2 TraesCS5D01G148600 chr5B 92.623 366 21 4 4976 5335 268436613 268436978 6.120000e-144 521
3 TraesCS5D01G148600 chr5A 92.586 4532 161 87 1 4388 318754248 318758748 0.000000e+00 6346
4 TraesCS5D01G148600 chr5A 92.784 388 17 6 4946 5332 318811564 318811941 7.810000e-153 551
5 TraesCS5D01G148600 chr5A 90.938 320 9 9 4421 4725 318758743 318759057 3.840000e-111 412
6 TraesCS5D01G148600 chr5A 95.506 89 3 1 3973 4061 25130112 25130199 2.000000e-29 141
7 TraesCS5D01G148600 chr4B 76.585 615 86 34 1365 1957 149938805 149938227 8.750000e-73 285
8 TraesCS5D01G148600 chr4B 92.432 185 14 0 2079 2263 149938143 149937959 1.140000e-66 265
9 TraesCS5D01G148600 chr4B 92.262 168 10 3 1065 1229 149939084 149938917 8.930000e-58 235
10 TraesCS5D01G148600 chr4D 76.144 612 95 26 1365 1957 106416712 106416133 1.890000e-69 274
11 TraesCS5D01G148600 chr4D 92.432 185 14 0 2079 2263 106416049 106415865 1.140000e-66 265
12 TraesCS5D01G148600 chr4D 91.667 168 11 3 1065 1229 106416991 106416824 4.160000e-56 230
13 TraesCS5D01G148600 chr4D 95.506 89 3 1 3973 4061 490887596 490887683 2.000000e-29 141
14 TraesCS5D01G148600 chr4A 92.973 185 13 0 2079 2263 469513121 469513305 2.450000e-68 270
15 TraesCS5D01G148600 chr4A 92.262 168 10 3 1065 1229 469512189 469512356 8.930000e-58 235
16 TraesCS5D01G148600 chr4A 78.370 319 44 9 1365 1668 469512468 469512776 3.280000e-42 183
17 TraesCS5D01G148600 chr2B 92.233 103 8 0 2631 2733 86212610 86212712 4.310000e-31 147
18 TraesCS5D01G148600 chrUn 95.506 89 3 1 3973 4061 345163363 345163450 2.000000e-29 141
19 TraesCS5D01G148600 chr6D 95.506 89 3 1 3973 4061 378804445 378804358 2.000000e-29 141
20 TraesCS5D01G148600 chr3D 95.506 89 3 1 3973 4061 206172616 206172703 2.000000e-29 141
21 TraesCS5D01G148600 chr2D 91.262 103 9 0 2631 2733 55058953 55059055 2.000000e-29 141
22 TraesCS5D01G148600 chr2A 90.291 103 10 0 2631 2733 55852821 55852923 9.320000e-28 135
23 TraesCS5D01G148600 chr2A 94.382 89 4 1 3973 4061 303670599 303670686 9.320000e-28 135
24 TraesCS5D01G148600 chr7A 93.258 89 5 1 3973 4061 376784035 376783948 4.340000e-26 130


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 TraesCS5D01G148600 chr5D 236660060 236665394 5334 True 9852.000000 9852 100.000000 1 5335 1 chr5D.!!$R1 5334
1 TraesCS5D01G148600 chr5B 268429845 268436978 7133 False 3739.000000 6957 92.429000 1 5335 2 chr5B.!!$F1 5334
2 TraesCS5D01G148600 chr5A 318754248 318759057 4809 False 3379.000000 6346 91.762000 1 4725 2 chr5A.!!$F3 4724
3 TraesCS5D01G148600 chr4B 149937959 149939084 1125 True 261.666667 285 87.093000 1065 2263 3 chr4B.!!$R1 1198
4 TraesCS5D01G148600 chr4D 106415865 106416991 1126 True 256.333333 274 86.747667 1065 2263 3 chr4D.!!$R1 1198
5 TraesCS5D01G148600 chr4A 469512189 469513305 1116 False 229.333333 270 87.868333 1065 2263 3 chr4A.!!$F1 1198

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
374 377 1.300971 AAGCGTCATTGCTGCATCGT 61.301 50.000 1.84 0.00 46.60 3.73 F
1059 1119 1.396301 CGAAAGCAGACTGCCATCTTC 59.604 52.381 23.74 18.15 46.52 2.87 F
1570 1654 1.448540 CACCGAGCAGGACATGGAC 60.449 63.158 5.19 0.00 45.00 4.02 F
2833 2960 1.097232 TTCATTTGGAGGATGCTGCG 58.903 50.000 0.47 0.00 0.00 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2002 2113 0.661483 GCTTGCTGCTTGAACGGAAC 60.661 55.000 0.0 0.0 38.95 3.62 R
2282 2399 3.317150 GGAAAGTGGAAAAGGAAATGCG 58.683 45.455 0.0 0.0 0.00 4.73 R
3500 3672 1.713647 TGATCCCACCCTTTGCCTTTA 59.286 47.619 0.0 0.0 0.00 1.85 R
4556 4799 0.179113 CAACAACTGGCCACCACAAC 60.179 55.000 0.0 0.0 0.00 3.32 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
147 148 8.349245 TGAACTGGTTGTGTTGTTATTTATGAG 58.651 33.333 0.00 0.00 0.00 2.90
280 283 2.048222 GTCGCACACTAGCTGGCA 60.048 61.111 0.00 0.00 0.00 4.92
281 284 2.048222 TCGCACACTAGCTGGCAC 60.048 61.111 0.00 0.00 0.00 5.01
330 333 4.968259 TGCACCAGTCAAAGTATAACTGT 58.032 39.130 0.00 0.00 38.97 3.55
374 377 1.300971 AAGCGTCATTGCTGCATCGT 61.301 50.000 1.84 0.00 46.60 3.73
444 447 9.100554 TCGTTATTTACACCAACCATAATACAG 57.899 33.333 0.00 0.00 0.00 2.74
451 454 2.354510 CCAACCATAATACAGCACCGTG 59.645 50.000 0.00 0.00 0.00 4.94
542 548 7.849804 AGTATTGGAATGAACTGACACATAC 57.150 36.000 0.00 0.00 0.00 2.39
547 553 5.643348 TGGAATGAACTGACACATACACATC 59.357 40.000 0.00 0.00 0.00 3.06
565 571 5.241285 ACACATCTAACATTGTGCACAATCA 59.759 36.000 36.19 24.05 45.59 2.57
594 607 1.614317 CGGAGAACCAAAGCCAAGGAT 60.614 52.381 0.00 0.00 35.59 3.24
618 631 3.852286 ACAACGGCGAACTATTGTGATA 58.148 40.909 16.62 0.00 34.08 2.15
623 636 6.764877 ACGGCGAACTATTGTGATATTTAG 57.235 37.500 16.62 0.00 0.00 1.85
630 643 8.939929 CGAACTATTGTGATATTTAGGCATCAT 58.060 33.333 0.00 0.00 33.92 2.45
649 663 7.043565 GCATCATCAAAAATTGTCCCACTAAT 58.956 34.615 0.00 0.00 0.00 1.73
690 704 6.549364 AGACCACCAAAATAACTCAAACATGA 59.451 34.615 0.00 0.00 0.00 3.07
726 757 4.873746 TGACCAAACCAACAACTCAAAA 57.126 36.364 0.00 0.00 0.00 2.44
782 823 4.283403 GGCGCACAAGCAAAGCCA 62.283 61.111 10.83 0.00 42.29 4.75
836 877 7.459795 AAAACCAAGCCAAAAATTTGAAAGA 57.540 28.000 7.44 0.00 40.55 2.52
837 878 6.682423 AACCAAGCCAAAAATTTGAAAGAG 57.318 33.333 7.44 0.00 40.55 2.85
1031 1082 1.606313 CCCCATCAAAACCGCACCT 60.606 57.895 0.00 0.00 0.00 4.00
1057 1117 3.149899 CGAAAGCAGACTGCCATCT 57.850 52.632 23.74 5.87 46.52 2.90
1058 1118 1.446907 CGAAAGCAGACTGCCATCTT 58.553 50.000 23.74 11.97 46.52 2.40
1059 1119 1.396301 CGAAAGCAGACTGCCATCTTC 59.604 52.381 23.74 18.15 46.52 2.87
1060 1120 1.742268 GAAAGCAGACTGCCATCTTCC 59.258 52.381 23.74 0.00 46.52 3.46
1570 1654 1.448540 CACCGAGCAGGACATGGAC 60.449 63.158 5.19 0.00 45.00 4.02
1737 1836 4.143543 CCCCAAGATTGCATTTTTGGTTT 58.856 39.130 22.34 0.00 38.69 3.27
1808 1912 2.361610 ATGCTTCTTGGCGGTGGG 60.362 61.111 0.00 0.00 34.52 4.61
1962 2069 4.293102 TGTCCTCCTACTTCAGGTACCTTA 59.707 45.833 13.15 0.20 45.71 2.69
2002 2113 2.515523 CCATGGCCGCTCTCCTTG 60.516 66.667 0.00 0.00 0.00 3.61
2058 2175 8.792830 TTTCTTTCCTAACAATGAGAATCGAT 57.207 30.769 0.00 0.00 38.61 3.59
2313 2430 1.740296 CCACTTTCCGCCGTCGAAT 60.740 57.895 0.00 0.00 38.10 3.34
2833 2960 1.097232 TTCATTTGGAGGATGCTGCG 58.903 50.000 0.47 0.00 0.00 5.18
2850 2977 3.426292 GCTGCGATCCAAGGTTTTACTTC 60.426 47.826 0.00 0.00 0.00 3.01
2881 3008 6.705381 CCTCTTGATCTTGACATGTTATCCTC 59.295 42.308 0.00 0.00 0.00 3.71
3249 3402 2.453521 GGGAAAGGAAATAAAGGGCGT 58.546 47.619 0.00 0.00 0.00 5.68
3412 3584 1.672030 GCCCCAAAAGCCATTGCAC 60.672 57.895 0.00 0.00 41.13 4.57
3500 3672 5.527214 GCTTAACAAAGGCCAAAAGAAATGT 59.473 36.000 5.01 0.00 0.00 2.71
3527 3699 3.960102 GCAAAGGGTGGGATCATCATAAA 59.040 43.478 0.00 0.00 0.00 1.40
3528 3700 4.202151 GCAAAGGGTGGGATCATCATAAAC 60.202 45.833 0.00 0.00 0.00 2.01
3571 3743 6.189859 AGGAATGATTTCTCAACTAATGGCA 58.810 36.000 0.00 0.00 34.37 4.92
3591 3763 6.763355 TGGCAATTTTTAATGCTGGTTCTTA 58.237 32.000 0.00 0.00 42.20 2.10
3593 3765 7.882271 TGGCAATTTTTAATGCTGGTTCTTATT 59.118 29.630 0.00 0.00 42.20 1.40
3594 3766 8.177013 GGCAATTTTTAATGCTGGTTCTTATTG 58.823 33.333 0.00 0.00 42.20 1.90
3595 3767 8.720562 GCAATTTTTAATGCTGGTTCTTATTGT 58.279 29.630 0.00 0.00 39.46 2.71
3601 3773 9.691362 TTTAATGCTGGTTCTTATTGTTCTTTC 57.309 29.630 0.00 0.00 0.00 2.62
3602 3774 6.899393 ATGCTGGTTCTTATTGTTCTTTCA 57.101 33.333 0.00 0.00 0.00 2.69
3757 3947 2.752358 CTCTGCAGAACCAGCCCA 59.248 61.111 18.85 0.00 32.87 5.36
3773 3963 0.464373 CCCACGCTGGTAGCATCATT 60.464 55.000 0.00 0.00 42.58 2.57
3774 3964 0.659427 CCACGCTGGTAGCATCATTG 59.341 55.000 0.00 0.00 42.58 2.82
3887 4077 0.689623 AAGTGCCCAGGTGAGAGAAG 59.310 55.000 0.00 0.00 0.00 2.85
3894 4084 2.630158 CCAGGTGAGAGAAGCATCAAG 58.370 52.381 0.00 0.00 0.00 3.02
3904 4094 5.244755 AGAGAAGCATCAAGACCTTTCTTC 58.755 41.667 0.00 0.00 40.34 2.87
3906 4096 3.409026 AGCATCAAGACCTTTCTTCGT 57.591 42.857 0.00 0.00 40.34 3.85
3909 4099 4.023707 AGCATCAAGACCTTTCTTCGTTTG 60.024 41.667 0.00 0.00 40.34 2.93
3911 4101 5.505654 GCATCAAGACCTTTCTTCGTTTGAA 60.506 40.000 0.00 0.00 40.34 2.69
3927 4117 4.202010 CGTTTGAACCTTCCATGTTCTTGT 60.202 41.667 4.94 0.00 42.04 3.16
4050 4240 3.783082 CAGGGGTCTCCTTTCCTCTTAAT 59.217 47.826 0.00 0.00 45.47 1.40
4079 4278 2.598394 TCAGCAACCAAGCCCTGC 60.598 61.111 0.00 0.00 36.29 4.85
4081 4280 2.118951 AGCAACCAAGCCCTGCAT 59.881 55.556 0.00 0.00 38.58 3.96
4085 4284 0.037975 CAACCAAGCCCTGCATTGTC 60.038 55.000 0.00 0.00 0.00 3.18
4086 4285 0.178953 AACCAAGCCCTGCATTGTCT 60.179 50.000 0.00 0.00 0.00 3.41
4087 4286 0.698238 ACCAAGCCCTGCATTGTCTA 59.302 50.000 0.00 0.00 0.00 2.59
4088 4287 1.075374 ACCAAGCCCTGCATTGTCTAA 59.925 47.619 0.00 0.00 0.00 2.10
4089 4288 1.474077 CCAAGCCCTGCATTGTCTAAC 59.526 52.381 0.00 0.00 0.00 2.34
4091 4290 2.119801 AGCCCTGCATTGTCTAACAG 57.880 50.000 0.00 0.00 0.00 3.16
4094 4293 2.787473 CCTGCATTGTCTAACAGGGA 57.213 50.000 0.00 0.00 44.90 4.20
4095 4294 3.287867 CCTGCATTGTCTAACAGGGAT 57.712 47.619 0.00 0.00 44.90 3.85
4096 4295 3.209410 CCTGCATTGTCTAACAGGGATC 58.791 50.000 0.00 0.00 44.90 3.36
4097 4296 3.370846 CCTGCATTGTCTAACAGGGATCA 60.371 47.826 0.00 0.00 44.90 2.92
4098 4297 4.458397 CTGCATTGTCTAACAGGGATCAT 58.542 43.478 0.00 0.00 0.00 2.45
4099 4298 4.858850 TGCATTGTCTAACAGGGATCATT 58.141 39.130 0.00 0.00 0.00 2.57
4101 4300 4.883585 GCATTGTCTAACAGGGATCATTCA 59.116 41.667 0.00 0.00 0.00 2.57
4150 4366 3.372566 CCTTGGCCCTGATGGTTATGTTA 60.373 47.826 0.00 0.00 36.04 2.41
4154 4370 3.569701 GGCCCTGATGGTTATGTTATGTG 59.430 47.826 0.00 0.00 36.04 3.21
4169 4386 0.464373 ATGTGTATGCAGGGAAGCCG 60.464 55.000 0.00 0.00 0.00 5.52
4399 4631 6.405953 GCTGCTCCAAGAAGTAGTAGTAATCA 60.406 42.308 0.00 0.00 32.21 2.57
4421 4653 9.844257 AATCAAGAAGAAGAAGAAGAAGAAGAA 57.156 29.630 0.00 0.00 0.00 2.52
4423 4655 8.700051 TCAAGAAGAAGAAGAAGAAGAAGAAGA 58.300 33.333 0.00 0.00 0.00 2.87
4424 4656 9.323985 CAAGAAGAAGAAGAAGAAGAAGAAGAA 57.676 33.333 0.00 0.00 0.00 2.52
4485 4728 6.573664 TTGTATGCTGTGCTCTGTAATTTT 57.426 33.333 0.00 0.00 0.00 1.82
4552 4795 2.061578 TCCGTCCTGGTGTGTGTGT 61.062 57.895 0.00 0.00 39.52 3.72
4553 4796 1.887242 CCGTCCTGGTGTGTGTGTG 60.887 63.158 0.00 0.00 0.00 3.82
4554 4797 1.142965 CGTCCTGGTGTGTGTGTGA 59.857 57.895 0.00 0.00 0.00 3.58
4555 4798 0.875908 CGTCCTGGTGTGTGTGTGAG 60.876 60.000 0.00 0.00 0.00 3.51
4556 4799 0.532862 GTCCTGGTGTGTGTGTGAGG 60.533 60.000 0.00 0.00 0.00 3.86
4623 4866 6.349300 ACAGATATCGAAAGCAAACAGGTAT 58.651 36.000 0.00 0.00 0.00 2.73
4625 4868 7.985184 ACAGATATCGAAAGCAAACAGGTATAA 59.015 33.333 0.00 0.00 0.00 0.98
4626 4869 8.826710 CAGATATCGAAAGCAAACAGGTATAAA 58.173 33.333 0.00 0.00 0.00 1.40
4630 4873 5.642063 TCGAAAGCAAACAGGTATAAAGAGG 59.358 40.000 0.00 0.00 0.00 3.69
4781 5032 1.137825 CAGCGTCCGTCCTCTCTTC 59.862 63.158 0.00 0.00 0.00 2.87
4803 5054 1.830477 GCCCATGCCCTTGTCAAAATA 59.170 47.619 0.00 0.00 0.00 1.40
4858 5112 6.501781 CATCCTCTGCATCTTTACATTTTCC 58.498 40.000 0.00 0.00 0.00 3.13
4859 5113 5.819991 TCCTCTGCATCTTTACATTTTCCT 58.180 37.500 0.00 0.00 0.00 3.36
4860 5114 6.248433 TCCTCTGCATCTTTACATTTTCCTT 58.752 36.000 0.00 0.00 0.00 3.36
4886 5142 1.499007 TGCCCTTCTCCCTTTTCAACT 59.501 47.619 0.00 0.00 0.00 3.16
4902 5158 7.386025 CCTTTTCAACTTCCTTTTCATCATTCC 59.614 37.037 0.00 0.00 0.00 3.01
4903 5159 5.627499 TCAACTTCCTTTTCATCATTCCG 57.373 39.130 0.00 0.00 0.00 4.30
4908 5164 1.331756 CCTTTTCATCATTCCGGAGCG 59.668 52.381 3.34 0.00 0.00 5.03
4944 5200 8.632906 AGTCTGAATCAAAAATCTGAACTGAT 57.367 30.769 0.00 0.00 0.00 2.90
4947 5203 9.070179 TCTGAATCAAAAATCTGAACTGATGAA 57.930 29.630 0.00 0.00 0.00 2.57
4949 5205 9.687210 TGAATCAAAAATCTGAACTGATGAAAG 57.313 29.630 0.00 0.00 0.00 2.62
4950 5206 9.136952 GAATCAAAAATCTGAACTGATGAAAGG 57.863 33.333 0.00 0.00 0.00 3.11
4952 5208 5.397142 AAAATCTGAACTGATGAAAGGGC 57.603 39.130 0.00 0.00 0.00 5.19
4953 5209 3.726557 ATCTGAACTGATGAAAGGGCA 57.273 42.857 0.00 0.00 0.00 5.36
4955 5211 2.089980 CTGAACTGATGAAAGGGCAGG 58.910 52.381 0.00 0.00 34.05 4.85
4957 5213 0.613012 AACTGATGAAAGGGCAGGCC 60.613 55.000 4.33 4.33 34.05 5.19
4958 5214 1.305623 CTGATGAAAGGGCAGGCCT 59.694 57.895 10.54 10.54 36.10 5.19
4959 5215 0.324091 CTGATGAAAGGGCAGGCCTT 60.324 55.000 22.73 22.73 36.10 4.35
4960 5216 0.612732 TGATGAAAGGGCAGGCCTTG 60.613 55.000 28.35 0.00 36.10 3.61
4961 5217 0.323725 GATGAAAGGGCAGGCCTTGA 60.324 55.000 28.35 18.16 36.10 3.02
4962 5218 0.337428 ATGAAAGGGCAGGCCTTGAT 59.663 50.000 28.35 19.51 36.10 2.57
4964 5220 1.357420 TGAAAGGGCAGGCCTTGATAA 59.643 47.619 28.35 11.78 36.10 1.75
4965 5221 2.027385 GAAAGGGCAGGCCTTGATAAG 58.973 52.381 28.35 0.00 36.10 1.73
4966 5222 1.002857 AAGGGCAGGCCTTGATAAGT 58.997 50.000 27.20 0.77 36.10 2.24
4967 5223 1.002857 AGGGCAGGCCTTGATAAGTT 58.997 50.000 10.54 0.00 36.10 2.66
4968 5224 1.106285 GGGCAGGCCTTGATAAGTTG 58.894 55.000 0.00 0.00 36.10 3.16
4969 5225 1.340991 GGGCAGGCCTTGATAAGTTGA 60.341 52.381 0.00 0.00 36.10 3.18
4970 5226 2.446435 GGCAGGCCTTGATAAGTTGAA 58.554 47.619 0.00 0.00 0.00 2.69
4972 5228 3.084786 GCAGGCCTTGATAAGTTGAAGT 58.915 45.455 0.00 0.00 0.00 3.01
4973 5229 3.507622 GCAGGCCTTGATAAGTTGAAGTT 59.492 43.478 0.00 0.00 0.00 2.66
4974 5230 4.616835 GCAGGCCTTGATAAGTTGAAGTTG 60.617 45.833 0.00 0.00 0.00 3.16
4985 7036 2.158957 AGTTGAAGTTGAGCCAAGTCGA 60.159 45.455 0.00 0.00 0.00 4.20
4987 7038 2.210116 TGAAGTTGAGCCAAGTCGAAC 58.790 47.619 0.00 0.00 0.00 3.95
4988 7039 2.210116 GAAGTTGAGCCAAGTCGAACA 58.790 47.619 0.00 0.00 0.00 3.18
4989 7040 1.871080 AGTTGAGCCAAGTCGAACAG 58.129 50.000 0.00 0.00 0.00 3.16
4990 7041 0.235926 GTTGAGCCAAGTCGAACAGC 59.764 55.000 0.00 0.00 0.00 4.40
4991 7042 0.179059 TTGAGCCAAGTCGAACAGCA 60.179 50.000 0.00 0.00 0.00 4.41
4996 7047 1.266718 GCCAAGTCGAACAGCATTTCA 59.733 47.619 0.00 0.00 0.00 2.69
4997 7048 2.095059 GCCAAGTCGAACAGCATTTCAT 60.095 45.455 0.00 0.00 0.00 2.57
4998 7049 3.751621 CCAAGTCGAACAGCATTTCATC 58.248 45.455 0.00 0.00 0.00 2.92
5010 7066 1.134946 CATTTCATCCGGGTTCTTGCC 59.865 52.381 0.00 0.00 0.00 4.52
5012 7068 0.322456 TTCATCCGGGTTCTTGCCTG 60.322 55.000 0.00 0.00 34.71 4.85
5022 7079 0.905357 TTCTTGCCTGGGCTAGTCTC 59.095 55.000 19.06 0.00 42.79 3.36
5029 7086 2.588620 CCTGGGCTAGTCTCGATTACT 58.411 52.381 5.93 5.93 0.00 2.24
5100 7157 0.956633 ACACTGGCTGCATCTGTTTG 59.043 50.000 0.50 0.00 0.00 2.93
5101 7158 0.956633 CACTGGCTGCATCTGTTTGT 59.043 50.000 0.50 0.00 0.00 2.83
5103 7160 2.161012 CACTGGCTGCATCTGTTTGTAG 59.839 50.000 0.50 0.00 33.06 2.74
5150 7207 9.356433 CGCATGCAATAATTTTATAATCATGGA 57.644 29.630 19.57 1.33 31.86 3.41
5263 7320 2.566833 TGGTCAACATCTGGTCAAGG 57.433 50.000 0.00 0.00 0.00 3.61
5296 7353 0.036010 CCTCACCTCGCCTGTTCAAT 60.036 55.000 0.00 0.00 0.00 2.57
5317 7374 0.038744 AACAGGGCATCCACTTCCAG 59.961 55.000 0.00 0.00 34.83 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 3.874543 TGTTTATACGCCAATAGCCTGTG 59.125 43.478 0.00 0.00 38.78 3.66
280 283 1.897133 TGCTTCACGGTACATACCAGT 59.103 47.619 8.76 4.66 46.80 4.00
281 284 2.268298 GTGCTTCACGGTACATACCAG 58.732 52.381 8.76 4.09 46.80 4.00
294 297 1.436195 GGTGCAGTGAACGTGCTTCA 61.436 55.000 0.00 0.00 41.78 3.02
330 333 2.126463 GTGACAGCTAGTGCGCGA 60.126 61.111 12.10 0.00 45.42 5.87
451 454 5.199424 ACATTGTCGCTTCATACGTTAAC 57.801 39.130 0.00 0.00 0.00 2.01
464 467 2.976729 ACAACGTGTTTACATTGTCGC 58.023 42.857 0.00 0.00 29.30 5.19
509 512 7.330946 TCAGTTCATTCCAATACTTGTACTTCG 59.669 37.037 0.00 0.00 0.00 3.79
519 522 7.119116 TGTGTATGTGTCAGTTCATTCCAATAC 59.881 37.037 0.00 0.00 0.00 1.89
525 528 6.974932 AGATGTGTATGTGTCAGTTCATTC 57.025 37.500 0.00 0.00 0.00 2.67
534 537 6.128309 TGCACAATGTTAGATGTGTATGTGTC 60.128 38.462 7.62 0.00 46.68 3.67
536 539 6.023435 GTGCACAATGTTAGATGTGTATGTG 58.977 40.000 13.17 0.00 46.68 3.21
542 548 5.701855 TGATTGTGCACAATGTTAGATGTG 58.298 37.500 41.64 1.70 45.72 3.21
547 553 6.151004 TGAACATGATTGTGCACAATGTTAG 58.849 36.000 41.64 29.52 45.72 2.34
565 571 3.689649 GCTTTGGTTCTCCGTATGAACAT 59.310 43.478 12.26 0.00 43.84 2.71
594 607 2.485903 ACAATAGTTCGCCGTTGTGAA 58.514 42.857 0.00 0.00 38.62 3.18
618 631 7.049754 GGGACAATTTTTGATGATGCCTAAAT 58.950 34.615 0.00 0.00 0.00 1.40
623 636 3.934579 GTGGGACAATTTTTGATGATGCC 59.065 43.478 0.00 0.00 44.16 4.40
630 643 8.875168 ACCAAATATTAGTGGGACAATTTTTGA 58.125 29.630 10.30 0.00 44.16 2.69
637 651 5.893500 TCCAACCAAATATTAGTGGGACAA 58.106 37.500 9.62 0.00 44.16 3.18
638 652 5.505780 CTCCAACCAAATATTAGTGGGACA 58.494 41.667 9.62 0.00 39.39 4.02
649 663 4.165372 GGTGGTCTATCCTCCAACCAAATA 59.835 45.833 0.00 0.00 46.08 1.40
680 694 7.912056 TTCCAATCTTCTAGTCATGTTTGAG 57.088 36.000 0.00 0.00 30.85 3.02
726 757 1.004745 ACACCTGGATCGAGGCAAAAT 59.995 47.619 22.58 0.76 36.46 1.82
823 864 4.202315 CGGTTCCCCCTCTTTCAAATTTTT 60.202 41.667 0.00 0.00 0.00 1.94
828 869 1.142060 TCGGTTCCCCCTCTTTCAAA 58.858 50.000 0.00 0.00 0.00 2.69
831 872 2.281539 TTTTCGGTTCCCCCTCTTTC 57.718 50.000 0.00 0.00 0.00 2.62
832 873 2.176148 TCTTTTTCGGTTCCCCCTCTTT 59.824 45.455 0.00 0.00 0.00 2.52
835 876 1.613520 CCTCTTTTTCGGTTCCCCCTC 60.614 57.143 0.00 0.00 0.00 4.30
836 877 0.404426 CCTCTTTTTCGGTTCCCCCT 59.596 55.000 0.00 0.00 0.00 4.79
837 878 0.611062 CCCTCTTTTTCGGTTCCCCC 60.611 60.000 0.00 0.00 0.00 5.40
1031 1082 1.188219 AGTCTGCTTTCGCTCCTCCA 61.188 55.000 0.00 0.00 36.97 3.86
1058 1118 2.125326 CGTAGGCGTCCATGGAGGA 61.125 63.158 33.29 13.64 46.75 3.71
1059 1119 2.076622 CTCGTAGGCGTCCATGGAGG 62.077 65.000 26.72 26.72 39.49 4.30
1060 1120 1.360551 CTCGTAGGCGTCCATGGAG 59.639 63.158 16.81 10.69 39.49 3.86
1718 1817 6.927381 AGAGAGAAACCAAAAATGCAATCTTG 59.073 34.615 0.00 0.00 0.00 3.02
1737 1836 3.131933 GCAAGATTAGCACTGGAGAGAGA 59.868 47.826 0.00 0.00 0.00 3.10
1808 1912 3.027170 CTTGTGCATGTCGTCGCCC 62.027 63.158 0.00 0.00 0.00 6.13
2002 2113 0.661483 GCTTGCTGCTTGAACGGAAC 60.661 55.000 0.00 0.00 38.95 3.62
2282 2399 3.317150 GGAAAGTGGAAAAGGAAATGCG 58.683 45.455 0.00 0.00 0.00 4.73
2313 2430 4.270834 ACTGAAACGATCTACTGCTCCTA 58.729 43.478 0.00 0.00 0.00 2.94
2833 2960 5.181433 GGTGAGTGAAGTAAAACCTTGGATC 59.819 44.000 0.00 0.00 0.00 3.36
2850 2977 4.263018 TGTCAAGATCAAGAGGTGAGTG 57.737 45.455 0.00 0.00 40.43 3.51
2881 3008 4.827481 GCCATGGCATGCAAGAAG 57.173 55.556 32.08 8.29 41.49 2.85
2945 3076 8.350722 CCATTGATCAGTGATATTTCTTTCCAG 58.649 37.037 18.99 0.00 0.00 3.86
3249 3402 4.080919 ACTTTCTCCTATGCTATGTGTGCA 60.081 41.667 0.00 0.00 44.95 4.57
3298 3451 5.235831 AGAAGAAAAGCAATCAAGCAAAAGC 59.764 36.000 0.00 0.00 36.85 3.51
3382 3551 3.244387 GCTTTTGGGGCCTCATTTTGTTA 60.244 43.478 5.88 0.00 0.00 2.41
3412 3584 3.515901 GCCTATATACCCTGACCTCCTTG 59.484 52.174 0.00 0.00 0.00 3.61
3500 3672 1.713647 TGATCCCACCCTTTGCCTTTA 59.286 47.619 0.00 0.00 0.00 1.85
3527 3699 7.645058 TTCCTCAAGTTTCTTTCATCTTTGT 57.355 32.000 0.00 0.00 0.00 2.83
3528 3700 8.355169 TCATTCCTCAAGTTTCTTTCATCTTTG 58.645 33.333 0.00 0.00 0.00 2.77
3591 3763 5.733620 ACAATGCATCCTGAAAGAACAAT 57.266 34.783 0.00 0.00 34.07 2.71
3593 3765 6.839124 ATAACAATGCATCCTGAAAGAACA 57.161 33.333 0.00 0.00 34.07 3.18
3594 3766 7.989826 AGTATAACAATGCATCCTGAAAGAAC 58.010 34.615 0.00 0.00 34.07 3.01
3595 3767 9.851686 ATAGTATAACAATGCATCCTGAAAGAA 57.148 29.630 0.00 0.00 34.07 2.52
3597 3769 9.060347 ACATAGTATAACAATGCATCCTGAAAG 57.940 33.333 0.00 0.00 0.00 2.62
3601 3773 6.429078 AGCACATAGTATAACAATGCATCCTG 59.571 38.462 0.00 0.00 34.03 3.86
3602 3774 6.537355 AGCACATAGTATAACAATGCATCCT 58.463 36.000 0.00 0.00 34.03 3.24
3634 3820 8.791675 TGCAGTTCAGTTCAAACAATAATCATA 58.208 29.630 0.00 0.00 0.00 2.15
3757 3947 1.097547 GCCAATGATGCTACCAGCGT 61.098 55.000 0.00 0.00 46.26 5.07
3773 3963 3.225798 GGGCTGCTGTTGTTGCCA 61.226 61.111 0.00 0.00 46.53 4.92
3774 3964 2.914097 AGGGCTGCTGTTGTTGCC 60.914 61.111 0.00 0.00 44.22 4.52
3783 3973 2.677289 CCACCAGATGAGGGCTGCT 61.677 63.158 0.00 0.00 32.06 4.24
3848 4038 5.416952 CACTTGGAAGAAGCAGGATTTGTAT 59.583 40.000 0.00 0.00 0.00 2.29
3887 4077 4.024048 TCAAACGAAGAAAGGTCTTGATGC 60.024 41.667 0.00 0.00 44.42 3.91
3894 4084 4.261072 GGAAGGTTCAAACGAAGAAAGGTC 60.261 45.833 0.00 0.00 0.00 3.85
3911 4101 3.864789 ACAGACAAGAACATGGAAGGT 57.135 42.857 0.00 0.00 0.00 3.50
3927 4117 7.920160 TCATAATGTTACATCAAGCAACAGA 57.080 32.000 0.00 0.00 36.95 3.41
3970 4160 3.365536 AGGAGAGAACCTGAAGCGA 57.634 52.632 0.00 0.00 39.01 4.93
4050 4240 2.698274 TGGTTGCTGACACTTACTCTGA 59.302 45.455 0.00 0.00 0.00 3.27
4061 4251 2.924105 GCAGGGCTTGGTTGCTGAC 61.924 63.158 0.00 0.00 35.05 3.51
4079 4278 6.118170 AGTGAATGATCCCTGTTAGACAATG 58.882 40.000 0.00 0.00 0.00 2.82
4081 4280 5.762179 AGTGAATGATCCCTGTTAGACAA 57.238 39.130 0.00 0.00 0.00 3.18
4085 4284 5.363868 TGGAGTAGTGAATGATCCCTGTTAG 59.636 44.000 0.00 0.00 0.00 2.34
4086 4285 5.277250 TGGAGTAGTGAATGATCCCTGTTA 58.723 41.667 0.00 0.00 0.00 2.41
4087 4286 4.104086 TGGAGTAGTGAATGATCCCTGTT 58.896 43.478 0.00 0.00 0.00 3.16
4088 4287 3.724478 TGGAGTAGTGAATGATCCCTGT 58.276 45.455 0.00 0.00 0.00 4.00
4089 4288 4.970860 ATGGAGTAGTGAATGATCCCTG 57.029 45.455 0.00 0.00 0.00 4.45
4091 4290 7.009179 TCATAATGGAGTAGTGAATGATCCC 57.991 40.000 0.00 0.00 0.00 3.85
4092 4291 7.065563 GCATCATAATGGAGTAGTGAATGATCC 59.934 40.741 0.00 0.00 31.91 3.36
4093 4292 7.605309 TGCATCATAATGGAGTAGTGAATGATC 59.395 37.037 0.00 0.00 31.91 2.92
4094 4293 7.455891 TGCATCATAATGGAGTAGTGAATGAT 58.544 34.615 0.00 0.00 33.94 2.45
4095 4294 6.829849 TGCATCATAATGGAGTAGTGAATGA 58.170 36.000 0.00 0.00 33.19 2.57
4096 4295 7.500720 TTGCATCATAATGGAGTAGTGAATG 57.499 36.000 0.00 0.00 34.44 2.67
4097 4296 7.557358 TGTTTGCATCATAATGGAGTAGTGAAT 59.443 33.333 0.00 0.00 34.44 2.57
4098 4297 6.883756 TGTTTGCATCATAATGGAGTAGTGAA 59.116 34.615 0.00 0.00 34.44 3.18
4099 4298 6.413892 TGTTTGCATCATAATGGAGTAGTGA 58.586 36.000 0.00 0.00 34.44 3.41
4101 4300 6.653020 TCTGTTTGCATCATAATGGAGTAGT 58.347 36.000 0.00 0.00 34.44 2.73
4150 4366 0.464373 CGGCTTCCCTGCATACACAT 60.464 55.000 0.00 0.00 34.04 3.21
4154 4370 0.811616 CTCACGGCTTCCCTGCATAC 60.812 60.000 0.00 0.00 34.04 2.39
4169 4386 0.962356 CCACTTCATGGGGTGCTCAC 60.962 60.000 11.63 0.00 45.95 3.51
4188 4405 4.589908 TGTTAGAGCCTTTTCCTTCCATC 58.410 43.478 0.00 0.00 0.00 3.51
4189 4406 4.657814 TGTTAGAGCCTTTTCCTTCCAT 57.342 40.909 0.00 0.00 0.00 3.41
4220 4442 1.008327 TGCTCCTCTCTGGGGATTACA 59.992 52.381 0.00 0.00 39.16 2.41
4223 4445 1.344191 GCTGCTCCTCTCTGGGGATT 61.344 60.000 0.00 0.00 39.16 3.01
4229 4451 1.153862 GTGTCGCTGCTCCTCTCTG 60.154 63.158 0.00 0.00 0.00 3.35
4399 4631 9.898152 TTTCTTCTTCTTCTTCTTCTTCTTCTT 57.102 29.630 0.00 0.00 0.00 2.52
4416 4648 7.483059 CAGACACACAGTTTTCTTTTCTTCTTC 59.517 37.037 0.00 0.00 0.00 2.87
4418 4650 6.431234 ACAGACACACAGTTTTCTTTTCTTCT 59.569 34.615 0.00 0.00 0.00 2.85
4419 4651 6.612306 ACAGACACACAGTTTTCTTTTCTTC 58.388 36.000 0.00 0.00 0.00 2.87
4420 4652 6.431234 AGACAGACACACAGTTTTCTTTTCTT 59.569 34.615 0.00 0.00 0.00 2.52
4421 4653 5.940470 AGACAGACACACAGTTTTCTTTTCT 59.060 36.000 0.00 0.00 0.00 2.52
4423 4655 7.770897 AGATAGACAGACACACAGTTTTCTTTT 59.229 33.333 0.00 0.00 0.00 2.27
4424 4656 7.275920 AGATAGACAGACACACAGTTTTCTTT 58.724 34.615 0.00 0.00 0.00 2.52
4485 4728 5.157395 TCACCATTCTGAGATCCATCCATA 58.843 41.667 0.00 0.00 0.00 2.74
4552 4795 1.932156 AACTGGCCACCACAACCTCA 61.932 55.000 0.00 0.00 0.00 3.86
4553 4796 1.152756 AACTGGCCACCACAACCTC 60.153 57.895 0.00 0.00 0.00 3.85
4554 4797 1.455587 CAACTGGCCACCACAACCT 60.456 57.895 0.00 0.00 0.00 3.50
4555 4798 1.326951 AACAACTGGCCACCACAACC 61.327 55.000 0.00 0.00 0.00 3.77
4556 4799 0.179113 CAACAACTGGCCACCACAAC 60.179 55.000 0.00 0.00 0.00 3.32
4623 4866 2.927007 TCCACTCCTCTCTCCCTCTTTA 59.073 50.000 0.00 0.00 0.00 1.85
4625 4868 1.006639 GTCCACTCCTCTCTCCCTCTT 59.993 57.143 0.00 0.00 0.00 2.85
4626 4869 0.629058 GTCCACTCCTCTCTCCCTCT 59.371 60.000 0.00 0.00 0.00 3.69
4630 4873 2.614229 GCTTTTGTCCACTCCTCTCTCC 60.614 54.545 0.00 0.00 0.00 3.71
4725 4974 3.321111 GGCGATTCCACTAGGATTCTGTA 59.679 47.826 0.00 0.00 45.26 2.74
4727 4976 2.366916 AGGCGATTCCACTAGGATTCTG 59.633 50.000 0.00 0.00 45.26 3.02
4768 5019 1.682684 GGGCAGAAGAGAGGACGGA 60.683 63.158 0.00 0.00 0.00 4.69
4781 5032 1.186917 TTTGACAAGGGCATGGGCAG 61.187 55.000 0.00 0.00 43.71 4.85
4803 5054 3.702045 GGAGTACTAGCATGACCTTGTCT 59.298 47.826 0.00 0.00 33.15 3.41
4886 5142 3.016736 GCTCCGGAATGATGAAAAGGAA 58.983 45.455 5.23 0.00 0.00 3.36
4902 5158 3.914966 CAGACTTAAGCATATACGCTCCG 59.085 47.826 1.29 0.00 42.89 4.63
4903 5159 5.122512 TCAGACTTAAGCATATACGCTCC 57.877 43.478 1.29 0.00 42.89 4.70
4918 5174 8.455903 TCAGTTCAGATTTTTGATTCAGACTT 57.544 30.769 0.00 0.00 0.00 3.01
4949 5205 1.106285 CAACTTATCAAGGCCTGCCC 58.894 55.000 5.69 0.00 36.58 5.36
4950 5206 2.128771 TCAACTTATCAAGGCCTGCC 57.871 50.000 5.69 0.00 0.00 4.85
4952 5208 4.761739 TCAACTTCAACTTATCAAGGCCTG 59.238 41.667 5.69 0.00 0.00 4.85
4953 5209 4.985538 TCAACTTCAACTTATCAAGGCCT 58.014 39.130 0.00 0.00 0.00 5.19
4955 5211 4.379918 GGCTCAACTTCAACTTATCAAGGC 60.380 45.833 0.00 0.00 0.00 4.35
4957 5213 5.947228 TGGCTCAACTTCAACTTATCAAG 57.053 39.130 0.00 0.00 0.00 3.02
4958 5214 5.827797 ACTTGGCTCAACTTCAACTTATCAA 59.172 36.000 0.00 0.00 0.00 2.57
4959 5215 5.376625 ACTTGGCTCAACTTCAACTTATCA 58.623 37.500 0.00 0.00 0.00 2.15
4960 5216 5.389935 CGACTTGGCTCAACTTCAACTTATC 60.390 44.000 0.00 0.00 0.00 1.75
4961 5217 4.452455 CGACTTGGCTCAACTTCAACTTAT 59.548 41.667 0.00 0.00 0.00 1.73
4962 5218 3.807622 CGACTTGGCTCAACTTCAACTTA 59.192 43.478 0.00 0.00 0.00 2.24
4964 5220 2.158957 TCGACTTGGCTCAACTTCAACT 60.159 45.455 0.00 0.00 0.00 3.16
4965 5221 2.210116 TCGACTTGGCTCAACTTCAAC 58.790 47.619 0.00 0.00 0.00 3.18
4966 5222 2.612212 GTTCGACTTGGCTCAACTTCAA 59.388 45.455 0.00 0.00 0.00 2.69
4967 5223 2.210116 GTTCGACTTGGCTCAACTTCA 58.790 47.619 0.00 0.00 0.00 3.02
4968 5224 2.210116 TGTTCGACTTGGCTCAACTTC 58.790 47.619 0.00 0.00 0.00 3.01
4969 5225 2.213499 CTGTTCGACTTGGCTCAACTT 58.787 47.619 0.00 0.00 0.00 2.66
4970 5226 1.871080 CTGTTCGACTTGGCTCAACT 58.129 50.000 0.00 0.00 0.00 3.16
4972 5228 0.179059 TGCTGTTCGACTTGGCTCAA 60.179 50.000 0.00 0.00 0.00 3.02
4973 5229 0.035317 ATGCTGTTCGACTTGGCTCA 59.965 50.000 0.00 0.00 0.00 4.26
4974 5230 1.160137 AATGCTGTTCGACTTGGCTC 58.840 50.000 0.00 0.00 0.00 4.70
4985 7036 1.818674 GAACCCGGATGAAATGCTGTT 59.181 47.619 0.73 0.00 31.94 3.16
4987 7038 1.755179 AGAACCCGGATGAAATGCTG 58.245 50.000 0.73 0.00 29.44 4.41
4988 7039 2.094675 CAAGAACCCGGATGAAATGCT 58.905 47.619 0.73 0.00 29.44 3.79
4989 7040 1.469767 GCAAGAACCCGGATGAAATGC 60.470 52.381 0.73 2.30 0.00 3.56
4990 7041 1.134946 GGCAAGAACCCGGATGAAATG 59.865 52.381 0.73 0.00 0.00 2.32
4991 7042 1.005924 AGGCAAGAACCCGGATGAAAT 59.994 47.619 0.73 0.00 0.00 2.17
4996 7047 2.677228 CCAGGCAAGAACCCGGAT 59.323 61.111 0.73 0.00 0.00 4.18
4997 7048 3.646715 CCCAGGCAAGAACCCGGA 61.647 66.667 0.73 0.00 0.00 5.14
5010 7066 2.294791 CCAGTAATCGAGACTAGCCCAG 59.705 54.545 2.65 0.00 0.00 4.45
5012 7068 1.000052 GCCAGTAATCGAGACTAGCCC 60.000 57.143 8.80 0.00 0.00 5.19
5022 7079 1.752501 CTCGTTGCCGCCAGTAATCG 61.753 60.000 0.00 0.00 0.00 3.34
5029 7086 4.680237 CTCCACTCGTTGCCGCCA 62.680 66.667 0.00 0.00 0.00 5.69
5032 7089 2.811317 GCTCTCCACTCGTTGCCG 60.811 66.667 0.00 0.00 0.00 5.69
5046 7103 0.392193 CATGCCCCGGATATCTGCTC 60.392 60.000 0.73 0.00 0.00 4.26
5100 7157 7.998212 GCGCACAATGAAATTTAATAATGCTAC 59.002 33.333 16.47 8.85 31.22 3.58
5101 7158 7.704047 TGCGCACAATGAAATTTAATAATGCTA 59.296 29.630 5.66 7.48 31.22 3.49
5103 7160 6.703857 TGCGCACAATGAAATTTAATAATGC 58.296 32.000 5.66 11.54 31.22 3.56
5104 7161 7.319380 GCATGCGCACAATGAAATTTAATAATG 59.681 33.333 14.90 0.59 33.45 1.90
5164 7221 6.419791 TGTTTTCTTACTCCAACTTCAAGGA 58.580 36.000 0.00 0.00 0.00 3.36
5263 7320 3.350833 AGGTGAGGTGATGATTTGCTTC 58.649 45.455 0.00 0.00 0.00 3.86
5296 7353 0.038166 GGAAGTGGATGCCCTGTTGA 59.962 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.