Multiple sequence alignment - TraesCS2D01G251100

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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 TraesCS2D01G251100 chr2D 100.000 5444 0 0 1 5444 299894836 299889393 0.000000e+00 10054
1 TraesCS2D01G251100 chr2D 94.318 88 5 0 3734 3821 557267266 557267179 9.510000e-28 135
2 TraesCS2D01G251100 chr2B 95.039 2177 76 15 3281 5444 371163824 371165981 0.000000e+00 3393
3 TraesCS2D01G251100 chr2B 94.541 1264 38 5 830 2070 371161379 371162634 0.000000e+00 1923
4 TraesCS2D01G251100 chr2B 94.752 1067 45 10 2066 3123 371162762 371163826 0.000000e+00 1650
5 TraesCS2D01G251100 chr2B 96.344 848 14 7 1 842 371160515 371161351 0.000000e+00 1378
6 TraesCS2D01G251100 chr2B 94.565 92 4 1 3734 3824 529265345 529265436 2.040000e-29 141
7 TraesCS2D01G251100 chr2A 95.907 1295 39 5 3281 4575 376082960 376081680 0.000000e+00 2085
8 TraesCS2D01G251100 chr2A 96.437 870 19 6 904 1763 376086744 376085877 0.000000e+00 1424
9 TraesCS2D01G251100 chr2A 94.631 894 34 6 1 891 376101165 376100283 0.000000e+00 1373
10 TraesCS2D01G251100 chr2A 93.559 916 39 4 1751 2663 376084264 376083366 0.000000e+00 1347
11 TraesCS2D01G251100 chr2A 92.330 678 34 12 4654 5313 376080438 376079761 0.000000e+00 948
12 TraesCS2D01G251100 chr2A 96.822 409 11 2 2717 3123 376083366 376082958 0.000000e+00 682
13 TraesCS2D01G251100 chr2A 97.006 167 5 0 3120 3286 184561317 184561151 1.150000e-71 281
14 TraesCS2D01G251100 chr2A 97.959 147 1 2 5300 5444 376078375 376078229 2.520000e-63 254
15 TraesCS2D01G251100 chr2A 96.739 92 2 1 3734 3824 593655909 593656000 9.440000e-33 152
16 TraesCS2D01G251100 chr1B 87.549 257 23 4 1 256 27302842 27303090 6.900000e-74 289
17 TraesCS2D01G251100 chr1B 95.376 173 7 1 3120 3292 110319812 110319983 1.930000e-69 274
18 TraesCS2D01G251100 chr5B 95.954 173 6 1 3120 3292 411972028 411971857 4.150000e-71 279
19 TraesCS2D01G251100 chr5B 94.475 181 8 2 3120 3300 417945557 417945735 1.490000e-70 278
20 TraesCS2D01G251100 chr3B 95.954 173 6 1 3120 3292 553848924 553848753 4.150000e-71 279
21 TraesCS2D01G251100 chr3B 95.376 173 7 1 3120 3292 80587404 80587233 1.930000e-69 274
22 TraesCS2D01G251100 chr3B 94.565 92 5 0 3734 3825 680423382 680423291 5.680000e-30 143
23 TraesCS2D01G251100 chr3B 94.444 90 5 0 3732 3821 671866542 671866631 7.350000e-29 139
24 TraesCS2D01G251100 chr3B 94.382 89 5 0 3731 3819 126580062 126580150 2.640000e-28 137
25 TraesCS2D01G251100 chr6B 95.906 171 6 1 3122 3292 79388634 79388803 5.370000e-70 276
26 TraesCS2D01G251100 chr7B 95.376 173 7 1 3120 3292 48281315 48281144 1.930000e-69 274
27 TraesCS2D01G251100 chr4B 95.376 173 7 1 3120 3292 549841918 549841747 1.930000e-69 274
28 TraesCS2D01G251100 chr1A 87.050 139 14 2 131 269 20700283 20700149 2.630000e-33 154
29 TraesCS2D01G251100 chr4A 94.444 90 4 1 3734 3823 590111631 590111543 2.640000e-28 137


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 TraesCS2D01G251100 chr2D 299889393 299894836 5443 True 10054.000000 10054 100.000000 1 5444 1 chr2D.!!$R1 5443
1 TraesCS2D01G251100 chr2B 371160515 371165981 5466 False 2086.000000 3393 95.169000 1 5444 4 chr2B.!!$F2 5443
2 TraesCS2D01G251100 chr2A 376100283 376101165 882 True 1373.000000 1373 94.631000 1 891 1 chr2A.!!$R2 890
3 TraesCS2D01G251100 chr2A 376078229 376086744 8515 True 1123.333333 2085 95.502333 904 5444 6 chr2A.!!$R3 4540

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
812 819 1.076533 CGATGTCTCGGTTTGGGTCG 61.077 60.0 0.0 0.0 41.27 4.79 F
1131 1205 0.026803 GCGATTTGCTGCTCTTACCG 59.973 55.0 0.0 0.0 41.73 4.02 F
1538 1613 1.480789 GAGGGTCTCTGAAGGAGTCC 58.519 60.0 0.0 0.0 45.34 3.85 F
2151 3985 1.830279 CTGATGTCCTTGTGTGGCAT 58.170 50.0 0.0 0.0 0.00 4.40 F
3131 4970 0.105039 GATGCCTTGTACTCCCTCCG 59.895 60.0 0.0 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2383 4220 0.525761 AATCCAAACCACATTCGCCG 59.474 50.000 0.00 0.0 0.00 6.46 R
2437 4274 1.414919 TGTGCAGGACCGTACTTCTTT 59.585 47.619 0.00 0.0 0.00 2.52 R
2821 4658 1.536644 AACCCCACCTGGAAACCTAA 58.463 50.000 0.00 0.0 37.39 2.69 R
3888 5734 0.688487 AACAATTTGCTGCAGGGCAT 59.312 45.000 17.12 0.0 42.09 4.40 R
5114 8141 0.178921 AGGTGGTTCTGAGCCAGAGA 60.179 55.000 13.91 0.0 41.75 3.10 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
812 819 1.076533 CGATGTCTCGGTTTGGGTCG 61.077 60.000 0.00 0.00 41.27 4.79
819 826 1.302993 CGGTTTGGGTCGGACCATT 60.303 57.895 27.32 0.00 41.02 3.16
891 940 5.455392 CAACTGTTTGGAAGTTATGCTGAG 58.545 41.667 0.00 0.00 35.70 3.35
892 941 4.718961 ACTGTTTGGAAGTTATGCTGAGT 58.281 39.130 0.00 0.00 0.00 3.41
893 942 5.865085 ACTGTTTGGAAGTTATGCTGAGTA 58.135 37.500 0.00 0.00 0.00 2.59
894 943 5.701290 ACTGTTTGGAAGTTATGCTGAGTAC 59.299 40.000 0.00 0.00 0.00 2.73
895 944 5.616270 TGTTTGGAAGTTATGCTGAGTACA 58.384 37.500 0.00 0.00 0.00 2.90
896 945 6.058833 TGTTTGGAAGTTATGCTGAGTACAA 58.941 36.000 0.00 0.00 0.00 2.41
897 946 6.204688 TGTTTGGAAGTTATGCTGAGTACAAG 59.795 38.462 0.00 0.00 0.00 3.16
898 947 5.738619 TGGAAGTTATGCTGAGTACAAGA 57.261 39.130 0.00 0.00 0.00 3.02
1055 1123 2.234908 GCTCTGCTCCTCTCACCTTTAA 59.765 50.000 0.00 0.00 0.00 1.52
1071 1142 6.996282 TCACCTTTAACCCTAAAAGAAGACAG 59.004 38.462 0.00 0.00 36.27 3.51
1131 1205 0.026803 GCGATTTGCTGCTCTTACCG 59.973 55.000 0.00 0.00 41.73 4.02
1472 1547 5.070001 TCCGGTTGATTTGTCTGAATTTCT 58.930 37.500 0.00 0.00 0.00 2.52
1538 1613 1.480789 GAGGGTCTCTGAAGGAGTCC 58.519 60.000 0.00 0.00 45.34 3.85
1819 3519 7.885922 TGCCTACATTTACTACTTTTTGGATGA 59.114 33.333 0.00 0.00 0.00 2.92
1902 3602 2.066999 GGAGGGCATCGAGAAGGGT 61.067 63.158 0.00 0.00 0.00 4.34
2009 3709 6.192234 TCTAGTGATGGACTTTCTCGTAAC 57.808 41.667 0.00 0.00 35.96 2.50
2082 3913 4.045334 TGTCAATTAGGAAAGGACCCCAAT 59.955 41.667 0.00 0.00 0.00 3.16
2143 3977 3.877559 TCCTTATGTGCTGATGTCCTTG 58.122 45.455 0.00 0.00 0.00 3.61
2151 3985 1.830279 CTGATGTCCTTGTGTGGCAT 58.170 50.000 0.00 0.00 0.00 4.40
2226 4062 4.497473 TTCGTTGCAAAGGAAATCGATT 57.503 36.364 12.54 4.39 46.36 3.34
2227 4063 5.614923 TTCGTTGCAAAGGAAATCGATTA 57.385 34.783 11.83 0.00 46.36 1.75
2229 4065 6.189677 TCGTTGCAAAGGAAATCGATTAAT 57.810 33.333 11.83 0.00 37.84 1.40
2377 4214 4.072131 GGATTCAGTTTCTGCAGGTTGTA 58.928 43.478 15.13 2.03 0.00 2.41
2446 4283 9.871238 TGTCCTTCAGATATACAAAAGAAGTAC 57.129 33.333 0.00 0.00 32.68 2.73
2484 4321 5.505654 CGCAAAGACAACCTGACAATTACTT 60.506 40.000 0.00 0.00 0.00 2.24
2663 4500 4.743493 AGACCACAATGACAAAACACAAC 58.257 39.130 0.00 0.00 0.00 3.32
2681 4518 7.149569 ACACAACTGATGATCATGGTAAAAG 57.850 36.000 14.30 3.59 0.00 2.27
2821 4658 4.704540 TCTGTGAACCACATTTCTGTTTGT 59.295 37.500 0.00 0.00 43.71 2.83
3012 4850 7.333528 TCATTAGTGGCAAAAGCTATTTAGG 57.666 36.000 0.00 0.00 0.00 2.69
3021 4859 6.036470 GCAAAAGCTATTTAGGTTGGCTTAG 58.964 40.000 14.28 0.00 42.60 2.18
3023 4861 7.602753 CAAAAGCTATTTAGGTTGGCTTAGTT 58.397 34.615 3.01 0.00 42.60 2.24
3123 4962 9.542462 TTGTAATAACTCTATGATGCCTTGTAC 57.458 33.333 0.00 0.00 0.00 2.90
3124 4963 8.924303 TGTAATAACTCTATGATGCCTTGTACT 58.076 33.333 0.00 0.00 0.00 2.73
3125 4964 9.413048 GTAATAACTCTATGATGCCTTGTACTC 57.587 37.037 0.00 0.00 0.00 2.59
3126 4965 4.946478 ACTCTATGATGCCTTGTACTCC 57.054 45.455 0.00 0.00 0.00 3.85
3127 4966 3.643792 ACTCTATGATGCCTTGTACTCCC 59.356 47.826 0.00 0.00 0.00 4.30
3128 4967 3.900601 CTCTATGATGCCTTGTACTCCCT 59.099 47.826 0.00 0.00 0.00 4.20
3129 4968 3.898123 TCTATGATGCCTTGTACTCCCTC 59.102 47.826 0.00 0.00 0.00 4.30
3130 4969 1.204146 TGATGCCTTGTACTCCCTCC 58.796 55.000 0.00 0.00 0.00 4.30
3131 4970 0.105039 GATGCCTTGTACTCCCTCCG 59.895 60.000 0.00 0.00 0.00 4.63
3132 4971 0.617820 ATGCCTTGTACTCCCTCCGT 60.618 55.000 0.00 0.00 0.00 4.69
3133 4972 0.834687 TGCCTTGTACTCCCTCCGTT 60.835 55.000 0.00 0.00 0.00 4.44
3134 4973 0.108281 GCCTTGTACTCCCTCCGTTC 60.108 60.000 0.00 0.00 0.00 3.95
3135 4974 0.535797 CCTTGTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
3136 4975 1.558233 CTTGTACTCCCTCCGTTCCT 58.442 55.000 0.00 0.00 0.00 3.36
3137 4976 2.622452 CCTTGTACTCCCTCCGTTCCTA 60.622 54.545 0.00 0.00 0.00 2.94
3138 4977 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3139 4978 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3140 4979 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3141 4980 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3142 4981 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3143 4982 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
3144 4983 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
3145 4984 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3146 4985 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3147 4986 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3148 4987 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3149 4988 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3150 4989 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3151 4990 7.656542 CCCTCCGTTCCTAAATATAAGTCTTTC 59.343 40.741 0.00 0.00 0.00 2.62
3152 4991 8.422566 CCTCCGTTCCTAAATATAAGTCTTTCT 58.577 37.037 0.00 0.00 0.00 2.52
3179 5018 8.307483 AGAGATTTCAATATGGACTACATACGG 58.693 37.037 0.00 0.00 44.41 4.02
3180 5019 8.190326 AGATTTCAATATGGACTACATACGGA 57.810 34.615 0.00 0.00 44.41 4.69
3181 5020 8.307483 AGATTTCAATATGGACTACATACGGAG 58.693 37.037 0.00 0.00 44.41 4.63
3182 5021 5.386958 TCAATATGGACTACATACGGAGC 57.613 43.478 0.00 0.00 44.41 4.70
3183 5022 4.830600 TCAATATGGACTACATACGGAGCA 59.169 41.667 0.00 0.00 44.41 4.26
3184 5023 5.303333 TCAATATGGACTACATACGGAGCAA 59.697 40.000 0.00 0.00 44.41 3.91
3185 5024 5.801531 ATATGGACTACATACGGAGCAAA 57.198 39.130 0.00 0.00 44.41 3.68
3186 5025 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
3187 5026 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
3188 5027 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
3189 5028 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
3190 5029 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
3191 5030 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3192 5031 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3193 5032 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3194 5033 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3195 5034 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3196 5035 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3197 5036 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3198 5037 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3199 5038 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3200 5039 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3201 5040 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3243 5082 6.911250 ACATCCGTATGTAGTCCATATTGA 57.089 37.500 0.00 0.00 44.66 2.57
3244 5083 7.297936 ACATCCGTATGTAGTCCATATTGAA 57.702 36.000 0.00 0.00 44.66 2.69
3245 5084 7.732025 ACATCCGTATGTAGTCCATATTGAAA 58.268 34.615 0.00 0.00 44.66 2.69
3246 5085 8.375506 ACATCCGTATGTAGTCCATATTGAAAT 58.624 33.333 0.00 0.00 44.66 2.17
3247 5086 8.873830 CATCCGTATGTAGTCCATATTGAAATC 58.126 37.037 0.00 0.00 38.29 2.17
3248 5087 8.190326 TCCGTATGTAGTCCATATTGAAATCT 57.810 34.615 0.00 0.00 38.29 2.40
3249 5088 8.304596 TCCGTATGTAGTCCATATTGAAATCTC 58.695 37.037 0.00 0.00 38.29 2.75
3250 5089 8.307483 CCGTATGTAGTCCATATTGAAATCTCT 58.693 37.037 0.00 0.00 38.29 3.10
3278 5117 9.508642 GAAAGACTTATATTTAGGAATGGAGGG 57.491 37.037 0.00 0.00 0.00 4.30
3279 5118 8.814448 AAGACTTATATTTAGGAATGGAGGGA 57.186 34.615 0.00 0.00 0.00 4.20
3280 5119 8.442660 AGACTTATATTTAGGAATGGAGGGAG 57.557 38.462 0.00 0.00 0.00 4.30
3281 5120 8.019652 AGACTTATATTTAGGAATGGAGGGAGT 58.980 37.037 0.00 0.00 0.00 3.85
3282 5121 9.322769 GACTTATATTTAGGAATGGAGGGAGTA 57.677 37.037 0.00 0.00 0.00 2.59
3293 5132 6.542735 GGAATGGAGGGAGTAGTTTGTAAATC 59.457 42.308 0.00 0.00 0.00 2.17
3604 5443 3.119352 GCAAATGTTTGGACTGATCTCCC 60.119 47.826 7.51 0.00 38.57 4.30
3675 5514 2.959516 GCTTTTGCTTCACCCAATACC 58.040 47.619 0.00 0.00 43.35 2.73
3697 5536 4.378459 CCGCATTGGTTTTCTGAAGTAGAC 60.378 45.833 0.00 0.00 34.43 2.59
3733 5572 8.564574 TGCTATTTCTGTTCGAAACAATAAACT 58.435 29.630 0.00 0.00 43.90 2.66
3760 5599 8.033626 ACTCCCTCTGTAACTTTTTATAAGTCG 58.966 37.037 0.00 0.00 0.00 4.18
3843 5682 6.956299 AAATTAGATGTGTGCTTGAAATGC 57.044 33.333 0.00 0.00 37.54 3.56
3858 5697 7.543172 TGCTTGAAATGCTGTCTTTATCAAATC 59.457 33.333 0.00 0.00 37.94 2.17
3888 5734 8.001881 TCTGACCACTTGCAATTAAAGTTTTA 57.998 30.769 0.00 0.00 35.70 1.52
3893 5739 6.128309 CCACTTGCAATTAAAGTTTTATGCCC 60.128 38.462 0.00 0.00 35.70 5.36
3961 5807 4.006319 ACTATTCTTTGTTGCTCTGCTCC 58.994 43.478 0.00 0.00 0.00 4.70
4036 5882 0.531311 ACTGTTCGTGGACCGGAAAC 60.531 55.000 9.46 1.60 37.11 2.78
4063 5909 3.398406 TCTCGTATTCTTTTGCTGTGCA 58.602 40.909 0.00 0.00 36.47 4.57
4095 5941 4.054359 ACTGTGACTCTTACCTCCAGAT 57.946 45.455 0.00 0.00 0.00 2.90
4469 6315 6.833342 ATGCAGAGTGAATTGTTTTGAAAC 57.167 33.333 0.00 0.00 39.33 2.78
4559 6405 9.683069 TCTTCTAATTTGACAAGCTTCAATTTC 57.317 29.630 10.17 0.00 35.42 2.17
4579 6425 3.792401 TCGAAATGGCATCGTATGTTCT 58.208 40.909 10.01 0.00 40.99 3.01
4583 6429 5.447144 CGAAATGGCATCGTATGTTCTTTCA 60.447 40.000 0.00 0.00 35.64 2.69
4589 6435 4.201950 GCATCGTATGTTCTTTCATGCCTT 60.202 41.667 0.00 0.00 0.00 4.35
4699 7708 1.567357 AGTCCAGAGAGAAAGGAGCC 58.433 55.000 0.00 0.00 30.78 4.70
4781 7793 6.031751 TCATAAAAGGGCACAACCAATTAC 57.968 37.500 0.00 0.00 42.05 1.89
4827 7841 6.554334 ACAATATACAAAACACTTCTGCGT 57.446 33.333 0.00 0.00 0.00 5.24
4832 7846 9.769093 AATATACAAAACACTTCTGCGTAATTC 57.231 29.630 0.00 0.00 0.00 2.17
4833 7847 4.855531 ACAAAACACTTCTGCGTAATTCC 58.144 39.130 0.00 0.00 0.00 3.01
4835 7849 4.749245 AAACACTTCTGCGTAATTCCAG 57.251 40.909 0.00 0.00 0.00 3.86
4838 7852 5.339008 ACACTTCTGCGTAATTCCAGATA 57.661 39.130 4.76 0.00 37.87 1.98
4840 7854 5.755375 ACACTTCTGCGTAATTCCAGATATG 59.245 40.000 4.76 7.93 37.87 1.78
4842 7856 5.755375 ACTTCTGCGTAATTCCAGATATGTG 59.245 40.000 4.76 0.00 37.87 3.21
4844 7858 4.060900 CTGCGTAATTCCAGATATGTGCT 58.939 43.478 0.00 0.00 0.00 4.40
4845 7859 5.010617 TCTGCGTAATTCCAGATATGTGCTA 59.989 40.000 0.00 0.00 33.44 3.49
4847 7861 4.627467 GCGTAATTCCAGATATGTGCTAGG 59.373 45.833 0.00 0.00 0.00 3.02
4848 7862 5.566826 GCGTAATTCCAGATATGTGCTAGGA 60.567 44.000 0.00 0.00 0.00 2.94
4850 7864 6.294787 CGTAATTCCAGATATGTGCTAGGAGT 60.295 42.308 0.00 0.00 0.00 3.85
4851 7865 6.506538 AATTCCAGATATGTGCTAGGAGTT 57.493 37.500 0.00 0.00 0.00 3.01
4945 7969 4.043750 TGCGTCAAAATTTTTGCTCAGAG 58.956 39.130 15.52 0.00 0.00 3.35
4971 7995 3.091545 ACATCTTGAATTGGAACGGCAT 58.908 40.909 0.00 0.00 0.00 4.40
5031 8055 8.801882 ATCATCTCTACCTGTCTATTAGTAGC 57.198 38.462 0.00 0.00 33.70 3.58
5072 8096 4.574828 TGTCTGTAAGTTGCTCTTTTCCAC 59.425 41.667 0.68 0.00 37.56 4.02
5114 8141 6.645415 CCTGAAGTAGTACTGTTTTTGTCGAT 59.355 38.462 5.39 0.00 0.00 3.59
5381 9808 8.371571 TGATTACTGATCTATCCATGCATAGT 57.628 34.615 0.00 0.00 35.69 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 187 0.249911 AGCTCACCAACAGGTTCGTC 60.250 55.000 0.00 0.00 31.84 4.20
431 434 2.345880 TATTTCGGCTCCGCGACTCC 62.346 60.000 8.23 3.78 39.59 3.85
432 435 1.065273 TATTTCGGCTCCGCGACTC 59.935 57.895 8.23 0.00 39.59 3.36
433 436 1.226888 GTATTTCGGCTCCGCGACT 60.227 57.895 8.23 0.00 39.59 4.18
434 437 2.235699 GGTATTTCGGCTCCGCGAC 61.236 63.158 8.23 0.00 39.59 5.19
435 438 2.105528 GGTATTTCGGCTCCGCGA 59.894 61.111 8.23 0.00 39.59 5.87
436 439 1.949631 GAGGTATTTCGGCTCCGCG 60.950 63.158 0.00 0.00 39.59 6.46
812 819 3.117512 ACCCATCATAAGTCCAATGGTCC 60.118 47.826 0.00 0.00 37.54 4.46
819 826 1.407618 CGACGACCCATCATAAGTCCA 59.592 52.381 0.00 0.00 0.00 4.02
891 940 1.660167 GGCCGTTATGGGTCTTGTAC 58.340 55.000 0.00 0.00 38.63 2.90
892 941 0.542805 GGGCCGTTATGGGTCTTGTA 59.457 55.000 0.00 0.00 38.63 2.41
893 942 1.301954 GGGCCGTTATGGGTCTTGT 59.698 57.895 0.00 0.00 38.63 3.16
894 943 0.322997 TTGGGCCGTTATGGGTCTTG 60.323 55.000 0.00 0.00 38.63 3.02
895 944 0.629058 ATTGGGCCGTTATGGGTCTT 59.371 50.000 0.00 0.00 38.63 3.01
896 945 0.182775 GATTGGGCCGTTATGGGTCT 59.817 55.000 0.00 0.00 38.63 3.85
897 946 0.106918 TGATTGGGCCGTTATGGGTC 60.107 55.000 0.00 0.00 38.63 4.46
898 947 0.395173 GTGATTGGGCCGTTATGGGT 60.395 55.000 0.00 0.00 38.63 4.51
1055 1123 6.544931 GTGGTTTTACTGTCTTCTTTTAGGGT 59.455 38.462 0.00 0.00 0.00 4.34
1071 1142 1.822506 GGGAGAGCAGGTGGTTTTAC 58.177 55.000 0.00 0.00 0.00 2.01
1131 1205 1.346068 AGAGGGTGAGCAGTCAGTTTC 59.654 52.381 0.00 0.00 31.53 2.78
1216 1290 1.512201 TACGGGTGGAGGGAGAAGGA 61.512 60.000 0.00 0.00 0.00 3.36
1538 1613 1.150567 CGATCTCAAGCGCTTCCCTG 61.151 60.000 22.21 10.48 0.00 4.45
1819 3519 5.094387 TCCACTCTCCTCAAACTCCTAAAT 58.906 41.667 0.00 0.00 0.00 1.40
1902 3602 8.679344 ACCATATGATCCATATACACACCTTA 57.321 34.615 3.65 0.00 35.18 2.69
2009 3709 5.449553 AGCAAAGATAAGGGTATCCAAAGG 58.550 41.667 0.00 0.00 37.43 3.11
2082 3913 9.187996 TCCATATTTCAGTAAGCAATGAATGAA 57.812 29.630 0.00 0.00 35.47 2.57
2143 3977 3.884693 TCATCATACAATGGATGCCACAC 59.115 43.478 0.00 0.00 40.50 3.82
2186 4020 7.413438 GCAACGAAAGATTATCAGATTGTGAGT 60.413 37.037 0.00 0.00 39.07 3.41
2206 4042 5.614923 TTAATCGATTTCCTTTGCAACGA 57.385 34.783 17.19 6.51 0.00 3.85
2261 4097 9.959749 CTTTTGCAAAGAATACCAACTAGTTTA 57.040 29.630 12.41 0.00 0.00 2.01
2265 4101 9.528018 TTTTCTTTTGCAAAGAATACCAACTAG 57.472 29.630 12.41 2.53 36.30 2.57
2267 4103 8.785329 TTTTTCTTTTGCAAAGAATACCAACT 57.215 26.923 12.41 0.00 36.30 3.16
2268 4104 8.878769 TCTTTTTCTTTTGCAAAGAATACCAAC 58.121 29.630 12.41 0.00 36.30 3.77
2269 4105 9.442047 TTCTTTTTCTTTTGCAAAGAATACCAA 57.558 25.926 12.41 6.95 40.15 3.67
2377 4214 2.434884 CCACATTCGCCGACTGCT 60.435 61.111 4.21 0.00 38.05 4.24
2383 4220 0.525761 AATCCAAACCACATTCGCCG 59.474 50.000 0.00 0.00 0.00 6.46
2389 4226 5.819991 AGTCTGTCATAATCCAAACCACAT 58.180 37.500 0.00 0.00 0.00 3.21
2437 4274 1.414919 TGTGCAGGACCGTACTTCTTT 59.585 47.619 0.00 0.00 0.00 2.52
2446 4283 2.741985 TGCGATTGTGCAGGACCG 60.742 61.111 0.00 0.00 40.62 4.79
2484 4321 8.624367 AATGAAAAATCATTCAGAAAATGCCA 57.376 26.923 0.00 0.00 42.21 4.92
2532 4369 4.584325 AGTTTTACTGCTTCAGCCAATTCA 59.416 37.500 0.00 0.00 41.18 2.57
2663 4500 5.821470 AGTGCTCTTTTACCATGATCATCAG 59.179 40.000 4.86 2.85 0.00 2.90
2681 4518 6.246420 ACAAAGATGTATGAAACAGTGCTC 57.754 37.500 0.00 0.00 42.70 4.26
2821 4658 1.536644 AACCCCACCTGGAAACCTAA 58.463 50.000 0.00 0.00 37.39 2.69
2962 4799 9.657419 AAAGAATGTTGTGATTCTGAAGTTTTT 57.343 25.926 0.00 0.00 41.02 1.94
2975 4812 5.534278 TGCCACTAATGAAAGAATGTTGTGA 59.466 36.000 0.00 0.00 0.00 3.58
3012 4850 4.568152 TCAGAAAAGCAACTAAGCCAAC 57.432 40.909 0.00 0.00 34.23 3.77
3021 4859 3.006217 AGGCTTTCCATCAGAAAAGCAAC 59.994 43.478 18.29 5.43 43.84 4.17
3023 4861 2.821969 GAGGCTTTCCATCAGAAAAGCA 59.178 45.455 18.29 0.00 43.84 3.91
3123 4962 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
3124 4963 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3125 4964 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3126 4965 8.422566 AGAAAGACTTATATTTAGGAACGGAGG 58.577 37.037 0.00 0.00 0.00 4.30
3153 4992 8.307483 CCGTATGTAGTCCATATTGAAATCTCT 58.693 37.037 0.00 0.00 38.29 3.10
3154 4993 8.304596 TCCGTATGTAGTCCATATTGAAATCTC 58.695 37.037 0.00 0.00 38.29 2.75
3155 4994 8.190326 TCCGTATGTAGTCCATATTGAAATCT 57.810 34.615 0.00 0.00 38.29 2.40
3156 4995 7.063544 GCTCCGTATGTAGTCCATATTGAAATC 59.936 40.741 0.00 0.00 38.29 2.17
3157 4996 6.874134 GCTCCGTATGTAGTCCATATTGAAAT 59.126 38.462 0.00 0.00 38.29 2.17
3158 4997 6.183360 TGCTCCGTATGTAGTCCATATTGAAA 60.183 38.462 0.00 0.00 38.29 2.69
3159 4998 5.303333 TGCTCCGTATGTAGTCCATATTGAA 59.697 40.000 0.00 0.00 38.29 2.69
3160 4999 4.830600 TGCTCCGTATGTAGTCCATATTGA 59.169 41.667 0.00 0.00 38.29 2.57
3161 5000 5.134202 TGCTCCGTATGTAGTCCATATTG 57.866 43.478 0.00 0.00 38.29 1.90
3162 5001 5.801531 TTGCTCCGTATGTAGTCCATATT 57.198 39.130 0.00 0.00 38.29 1.28
3163 5002 5.801531 TTTGCTCCGTATGTAGTCCATAT 57.198 39.130 0.00 0.00 38.29 1.78
3164 5003 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
3165 5004 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
3166 5005 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
3167 5006 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
3168 5007 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3169 5008 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3170 5009 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3171 5010 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3172 5011 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3173 5012 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3174 5013 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3175 5014 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3176 5015 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3177 5016 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3178 5017 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3179 5018 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3210 5049 9.339850 GGACTACATACGGATGTATATAGACAT 57.660 37.037 20.64 12.70 45.42 3.06
3211 5050 8.323567 TGGACTACATACGGATGTATATAGACA 58.676 37.037 20.64 12.12 45.42 3.41
3212 5051 8.728337 TGGACTACATACGGATGTATATAGAC 57.272 38.462 20.64 10.95 45.42 2.59
3217 5056 9.689501 TCAATATGGACTACATACGGATGTATA 57.310 33.333 20.64 11.30 45.42 1.47
3218 5057 8.589701 TCAATATGGACTACATACGGATGTAT 57.410 34.615 20.64 9.39 45.42 2.29
3219 5058 8.411991 TTCAATATGGACTACATACGGATGTA 57.588 34.615 19.32 19.32 44.77 2.29
3221 5060 8.777865 ATTTCAATATGGACTACATACGGATG 57.222 34.615 5.94 5.94 44.41 3.51
3222 5061 8.816894 AGATTTCAATATGGACTACATACGGAT 58.183 33.333 0.00 0.00 44.41 4.18
3223 5062 8.190326 AGATTTCAATATGGACTACATACGGA 57.810 34.615 0.00 0.00 44.41 4.69
3224 5063 8.307483 AGAGATTTCAATATGGACTACATACGG 58.693 37.037 0.00 0.00 44.41 4.02
3252 5091 9.508642 CCCTCCATTCCTAAATATAAGTCTTTC 57.491 37.037 0.00 0.00 0.00 2.62
3253 5092 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
3254 5093 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
3255 5094 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
3256 5095 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
3257 5096 9.327731 CTACTCCCTCCATTCCTAAATATAAGT 57.672 37.037 0.00 0.00 0.00 2.24
3258 5097 9.327731 ACTACTCCCTCCATTCCTAAATATAAG 57.672 37.037 0.00 0.00 0.00 1.73
3259 5098 9.684702 AACTACTCCCTCCATTCCTAAATATAA 57.315 33.333 0.00 0.00 0.00 0.98
3260 5099 9.684702 AAACTACTCCCTCCATTCCTAAATATA 57.315 33.333 0.00 0.00 0.00 0.86
3261 5100 8.440771 CAAACTACTCCCTCCATTCCTAAATAT 58.559 37.037 0.00 0.00 0.00 1.28
3262 5101 7.404980 ACAAACTACTCCCTCCATTCCTAAATA 59.595 37.037 0.00 0.00 0.00 1.40
3263 5102 6.217693 ACAAACTACTCCCTCCATTCCTAAAT 59.782 38.462 0.00 0.00 0.00 1.40
3264 5103 5.550403 ACAAACTACTCCCTCCATTCCTAAA 59.450 40.000 0.00 0.00 0.00 1.85
3265 5104 5.098663 ACAAACTACTCCCTCCATTCCTAA 58.901 41.667 0.00 0.00 0.00 2.69
3266 5105 4.695606 ACAAACTACTCCCTCCATTCCTA 58.304 43.478 0.00 0.00 0.00 2.94
3267 5106 3.532102 ACAAACTACTCCCTCCATTCCT 58.468 45.455 0.00 0.00 0.00 3.36
3268 5107 5.431179 TTACAAACTACTCCCTCCATTCC 57.569 43.478 0.00 0.00 0.00 3.01
3269 5108 7.110155 TGATTTACAAACTACTCCCTCCATTC 58.890 38.462 0.00 0.00 0.00 2.67
3270 5109 7.027874 TGATTTACAAACTACTCCCTCCATT 57.972 36.000 0.00 0.00 0.00 3.16
3271 5110 6.636454 TGATTTACAAACTACTCCCTCCAT 57.364 37.500 0.00 0.00 0.00 3.41
3272 5111 6.636454 ATGATTTACAAACTACTCCCTCCA 57.364 37.500 0.00 0.00 0.00 3.86
3273 5112 8.265764 AGTTATGATTTACAAACTACTCCCTCC 58.734 37.037 0.00 0.00 32.52 4.30
3274 5113 9.315525 GAGTTATGATTTACAAACTACTCCCTC 57.684 37.037 0.00 0.00 33.53 4.30
3275 5114 9.047947 AGAGTTATGATTTACAAACTACTCCCT 57.952 33.333 0.00 0.00 33.53 4.20
3276 5115 9.668497 AAGAGTTATGATTTACAAACTACTCCC 57.332 33.333 0.00 0.00 33.53 4.30
3282 5121 9.739276 TCCATGAAGAGTTATGATTTACAAACT 57.261 29.630 0.00 0.00 34.86 2.66
3293 5132 3.624861 GCAGTGGTCCATGAAGAGTTATG 59.375 47.826 0.00 0.00 0.00 1.90
3307 5146 2.618709 GCCATTAATACCTGCAGTGGTC 59.381 50.000 13.81 4.73 41.22 4.02
3604 5443 6.498304 ACTTGACATACAAAGTTGAAGCTTG 58.502 36.000 2.10 0.00 38.08 4.01
3675 5514 4.378459 GGTCTACTTCAGAAAACCAATGCG 60.378 45.833 0.00 0.00 34.17 4.73
3697 5536 6.483307 TCGAACAGAAATAGCATAAGGATTGG 59.517 38.462 0.00 0.00 0.00 3.16
3755 5594 5.607477 TGTCATGGACTCTAAAAACGACTT 58.393 37.500 0.00 0.00 33.15 3.01
3758 5597 4.988540 CACTGTCATGGACTCTAAAAACGA 59.011 41.667 0.00 0.00 33.15 3.85
3760 5599 5.758296 TGACACTGTCATGGACTCTAAAAAC 59.242 40.000 7.84 0.00 37.67 2.43
3790 5629 8.794553 ACTCCCTCTGTAACATAATATAAGACG 58.205 37.037 0.00 0.00 0.00 4.18
3802 5641 9.710818 ATCTAATTTACTACTCCCTCTGTAACA 57.289 33.333 0.00 0.00 0.00 2.41
3843 5682 8.233190 GGTCAGAACTTGATTTGATAAAGACAG 58.767 37.037 0.00 0.00 38.29 3.51
3888 5734 0.688487 AACAATTTGCTGCAGGGCAT 59.312 45.000 17.12 0.00 42.09 4.40
3893 5739 4.318974 GGCTAAACAAACAATTTGCTGCAG 60.319 41.667 10.11 10.11 44.39 4.41
4036 5882 5.406780 ACAGCAAAAGAATACGAGAAGTCAG 59.593 40.000 0.00 0.00 0.00 3.51
4063 5909 9.185680 AGGTAAGAGTCACAGTACAAAAATTTT 57.814 29.630 0.00 0.00 0.00 1.82
4068 5914 5.364446 TGGAGGTAAGAGTCACAGTACAAAA 59.636 40.000 0.00 0.00 0.00 2.44
4073 5919 4.652679 TCTGGAGGTAAGAGTCACAGTA 57.347 45.455 0.00 0.00 0.00 2.74
4076 5922 5.825593 AAAATCTGGAGGTAAGAGTCACA 57.174 39.130 0.00 0.00 0.00 3.58
4469 6315 4.374309 CGAAGAGCAAGCAAAAACGAAATG 60.374 41.667 0.00 0.00 0.00 2.32
4475 6321 2.492019 ACCGAAGAGCAAGCAAAAAC 57.508 45.000 0.00 0.00 0.00 2.43
4559 6405 4.536364 AAGAACATACGATGCCATTTCG 57.464 40.909 0.00 0.00 42.20 3.46
4579 6425 9.383519 CTGTACTTTAATCTCTAAGGCATGAAA 57.616 33.333 0.00 0.00 0.00 2.69
4699 7708 4.978580 GTCAGTTTTGCTTTTAGGCTCTTG 59.021 41.667 0.00 0.00 0.00 3.02
4819 7833 5.333645 GCACATATCTGGAATTACGCAGAAG 60.334 44.000 0.00 0.00 32.63 2.85
4820 7834 4.511454 GCACATATCTGGAATTACGCAGAA 59.489 41.667 0.00 0.00 32.63 3.02
4824 7838 4.627467 CCTAGCACATATCTGGAATTACGC 59.373 45.833 0.00 0.00 0.00 4.42
4826 7840 6.998802 ACTCCTAGCACATATCTGGAATTAC 58.001 40.000 0.00 0.00 0.00 1.89
4827 7841 7.290014 TCAACTCCTAGCACATATCTGGAATTA 59.710 37.037 0.00 0.00 0.00 1.40
4832 7846 4.944619 TCAACTCCTAGCACATATCTGG 57.055 45.455 0.00 0.00 0.00 3.86
4833 7847 5.011431 TGGATCAACTCCTAGCACATATCTG 59.989 44.000 0.00 0.00 45.21 2.90
4835 7849 5.244851 TCTGGATCAACTCCTAGCACATATC 59.755 44.000 0.00 0.00 45.21 1.63
4838 7852 3.378512 TCTGGATCAACTCCTAGCACAT 58.621 45.455 0.00 0.00 45.21 3.21
4840 7854 5.736951 ATATCTGGATCAACTCCTAGCAC 57.263 43.478 0.00 0.00 45.21 4.40
4842 7856 7.003402 AGAAATATCTGGATCAACTCCTAGC 57.997 40.000 0.00 0.00 45.21 3.42
4878 7898 7.228906 CGGACACTAGATTATTAGACTCTGGAA 59.771 40.741 0.00 0.00 0.00 3.53
4880 7900 6.487331 ACGGACACTAGATTATTAGACTCTGG 59.513 42.308 0.00 0.00 0.00 3.86
4881 7901 7.356540 CACGGACACTAGATTATTAGACTCTG 58.643 42.308 0.00 0.00 0.00 3.35
4945 7969 4.437390 CCGTTCCAATTCAAGATGTACTGC 60.437 45.833 0.00 0.00 0.00 4.40
4971 7995 2.693591 TGGTGCACCGGTTCAAAAATTA 59.306 40.909 30.07 5.45 39.43 1.40
5031 8055 5.046529 CAGACAACTGCCAGCTATTAGTAG 58.953 45.833 0.00 0.00 37.33 2.57
5072 8096 1.470098 CAGGACAATTTGAAGGCGAGG 59.530 52.381 2.79 0.00 0.00 4.63
5114 8141 0.178921 AGGTGGTTCTGAGCCAGAGA 60.179 55.000 13.91 0.00 41.75 3.10
5229 8256 6.237901 ACATGTTTACTGAATGCAGGAACTA 58.762 36.000 17.95 4.22 44.53 2.24


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

AutoCloner maintained by Alex Coulton.