Multiple sequence alignment - TraesCS5A01G308100

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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 TraesCS5A01G308100 chr5A 100.000 2300 0 0 1 2300 520660392 520662691 0.000000e+00 4248.0
1 TraesCS5A01G308100 chr5A 91.738 351 20 5 858 1206 607200243 607199900 1.600000e-131 479.0
2 TraesCS5A01G308100 chr5A 79.007 443 67 20 20 449 606011672 606012101 1.740000e-71 279.0
3 TraesCS5A01G308100 chr5A 78.231 441 68 21 23 449 582606338 582605912 8.150000e-65 257.0
4 TraesCS5A01G308100 chr5A 92.308 117 7 2 2185 2300 520604650 520604765 5.080000e-37 165.0
5 TraesCS5A01G308100 chr5A 83.333 120 15 4 491 606 606012183 606012301 3.130000e-19 106.0
6 TraesCS5A01G308100 chr5D 91.632 956 54 14 1208 2149 512416234 512415291 0.000000e+00 1299.0
7 TraesCS5A01G308100 chr5D 91.623 955 55 14 1208 2149 512409297 512408355 0.000000e+00 1297.0
8 TraesCS5A01G308100 chr5D 91.250 960 60 12 1203 2149 503287546 503288494 0.000000e+00 1286.0
9 TraesCS5A01G308100 chr5D 91.241 959 57 16 1203 2149 120800116 120801059 0.000000e+00 1280.0
10 TraesCS5A01G308100 chr5D 91.193 352 21 5 858 1206 6181099 6180755 9.620000e-129 470.0
11 TraesCS5A01G308100 chr5D 92.558 215 12 4 2088 2300 409436943 409437155 2.870000e-79 305.0
12 TraesCS5A01G308100 chr2B 91.414 955 52 18 1203 2149 474900589 474901521 0.000000e+00 1282.0
13 TraesCS5A01G308100 chr2B 91.404 349 20 5 858 1203 474900189 474900530 9.620000e-129 470.0
14 TraesCS5A01G308100 chr6D 91.232 958 56 16 1203 2149 45511323 45510383 0.000000e+00 1279.0
15 TraesCS5A01G308100 chr6D 91.477 352 20 5 858 1206 45511724 45511380 2.070000e-130 475.0
16 TraesCS5A01G308100 chr1D 91.118 957 63 14 1203 2149 51877827 51876883 0.000000e+00 1277.0
17 TraesCS5A01G308100 chr1D 91.099 955 58 15 1203 2149 254417312 254418247 0.000000e+00 1267.0
18 TraesCS5A01G308100 chr1D 91.453 351 21 4 858 1206 51878226 51877883 7.440000e-130 473.0
19 TraesCS5A01G308100 chr1D 86.364 66 9 0 22 87 423159979 423159914 3.170000e-09 73.1
20 TraesCS5A01G308100 chr1A 91.232 958 54 16 1203 2149 554458714 554459652 0.000000e+00 1277.0
21 TraesCS5A01G308100 chr1A 91.477 352 20 5 858 1206 554457094 554456750 2.070000e-130 475.0
22 TraesCS5A01G308100 chr1A 91.404 349 20 5 858 1203 554456052 554456393 9.620000e-129 470.0
23 TraesCS5A01G308100 chr1A 91.404 349 20 5 858 1203 554458314 554458655 9.620000e-129 470.0
24 TraesCS5A01G308100 chr7D 87.155 833 80 19 23 843 65753696 65752879 0.000000e+00 920.0
25 TraesCS5A01G308100 chr3B 91.193 352 21 5 858 1206 101919198 101918854 9.620000e-129 470.0
26 TraesCS5A01G308100 chr3A 77.184 618 94 26 23 606 19311854 19312458 1.330000e-82 316.0
27 TraesCS5A01G308100 chr4B 76.513 413 72 18 50 449 434600678 434600278 3.870000e-48 202.0
28 TraesCS5A01G308100 chr1B 83.043 230 32 6 222 449 596117362 596117586 3.870000e-48 202.0
29 TraesCS5A01G308100 chr1B 100.000 28 0 0 2263 2290 152519089 152519062 4.000000e-03 52.8


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 TraesCS5A01G308100 chr5A 520660392 520662691 2299 False 4248 4248 100.000000 1 2300 1 chr5A.!!$F2 2299
1 TraesCS5A01G308100 chr5D 512415291 512416234 943 True 1299 1299 91.632000 1208 2149 1 chr5D.!!$R3 941
2 TraesCS5A01G308100 chr5D 512408355 512409297 942 True 1297 1297 91.623000 1208 2149 1 chr5D.!!$R2 941
3 TraesCS5A01G308100 chr5D 503287546 503288494 948 False 1286 1286 91.250000 1203 2149 1 chr5D.!!$F3 946
4 TraesCS5A01G308100 chr5D 120800116 120801059 943 False 1280 1280 91.241000 1203 2149 1 chr5D.!!$F1 946
5 TraesCS5A01G308100 chr2B 474900189 474901521 1332 False 876 1282 91.409000 858 2149 2 chr2B.!!$F1 1291
6 TraesCS5A01G308100 chr6D 45510383 45511724 1341 True 877 1279 91.354500 858 2149 2 chr6D.!!$R1 1291
7 TraesCS5A01G308100 chr1D 254417312 254418247 935 False 1267 1267 91.099000 1203 2149 1 chr1D.!!$F1 946
8 TraesCS5A01G308100 chr1D 51876883 51878226 1343 True 875 1277 91.285500 858 2149 2 chr1D.!!$R2 1291
9 TraesCS5A01G308100 chr1A 554456052 554459652 3600 False 739 1277 91.346667 858 2149 3 chr1A.!!$F1 1291
10 TraesCS5A01G308100 chr7D 65752879 65753696 817 True 920 920 87.155000 23 843 1 chr7D.!!$R1 820
11 TraesCS5A01G308100 chr3A 19311854 19312458 604 False 316 316 77.184000 23 606 1 chr3A.!!$F1 583

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
153 154 0.038159 CCCTTTTCTCTCACGACGCT 60.038 55.0 0.0 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 4201 1.471119 ACTTCTCGCGTCCAGGATTA 58.529 50.0 5.77 0.0 0.0 1.75 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
43 44 2.553172 GGCGACTACTACGAATCATCCT 59.447 50.000 0.00 0.00 0.00 3.24
128 129 0.650512 ACGTCAAACACTCAACGCAG 59.349 50.000 0.00 0.00 38.64 5.18
146 147 1.349026 CAGGCTGACCCTTTTCTCTCA 59.651 52.381 9.42 0.00 43.06 3.27
149 150 1.000955 GCTGACCCTTTTCTCTCACGA 59.999 52.381 0.00 0.00 0.00 4.35
153 154 0.038159 CCCTTTTCTCTCACGACGCT 60.038 55.000 0.00 0.00 0.00 5.07
214 223 0.839277 AGCATCCATCCCATCAACGA 59.161 50.000 0.00 0.00 0.00 3.85
260 269 4.488136 CGCCATGCCTAGCCACCA 62.488 66.667 0.00 0.00 0.00 4.17
292 301 2.274760 GGAGCTGCAATGGAGCCT 59.725 61.111 22.86 10.51 37.12 4.58
364 395 0.743701 CGAAGCTCCATTGCAGCTCT 60.744 55.000 1.80 0.00 46.96 4.09
404 435 1.455217 GGGCAGAGCTCCAATGCAT 60.455 57.895 23.20 0.00 41.78 3.96
406 437 0.465824 GGCAGAGCTCCAATGCATCT 60.466 55.000 23.20 0.00 41.78 2.90
408 439 2.017623 GCAGAGCTCCAATGCATCTGT 61.018 52.381 18.64 0.00 38.83 3.41
428 460 4.800554 CGGAGCTCCAACAAACCT 57.199 55.556 31.67 0.00 35.14 3.50
470 502 2.658268 CGATGACGGCGCATGCTA 60.658 61.111 17.13 0.00 42.25 3.49
471 503 2.023771 CGATGACGGCGCATGCTAT 61.024 57.895 17.13 0.00 42.25 2.97
485 517 0.104671 TGCTATGATGCAGCACGCTA 59.895 50.000 23.13 6.61 43.90 4.26
488 520 2.204237 CTATGATGCAGCACGCTACAA 58.796 47.619 6.89 0.00 43.06 2.41
489 539 0.729116 ATGATGCAGCACGCTACAAC 59.271 50.000 6.89 0.00 43.06 3.32
541 593 2.271497 GGAGCTGCAGTGGAGCAT 59.729 61.111 34.21 20.98 44.68 3.79
571 623 2.158959 CGTGAGGCGACGATGGTTC 61.159 63.158 0.00 0.00 44.77 3.62
589 641 2.195741 TCGCTGTAGTGGTGTAGAGT 57.804 50.000 0.00 0.00 0.00 3.24
719 771 0.105778 GGAGGAGAAGAATGAGCGGG 59.894 60.000 0.00 0.00 0.00 6.13
724 776 2.003301 GAGAAGAATGAGCGGGTGAAC 58.997 52.381 0.00 0.00 0.00 3.18
747 799 3.456277 ACCTTCTGCGGGAAAGAGATAAT 59.544 43.478 0.00 0.00 33.07 1.28
763 815 5.124776 AGAGATAATCGAGCGGAAGGATAAG 59.875 44.000 0.00 0.00 0.00 1.73
765 817 1.705873 ATCGAGCGGAAGGATAAGGT 58.294 50.000 0.00 0.00 0.00 3.50
774 826 3.512496 GGAAGGATAAGGTAGGGAGAGG 58.488 54.545 0.00 0.00 0.00 3.69
779 831 4.933296 AGGATAAGGTAGGGAGAGGGATAA 59.067 45.833 0.00 0.00 0.00 1.75
780 832 5.016890 AGGATAAGGTAGGGAGAGGGATAAG 59.983 48.000 0.00 0.00 0.00 1.73
781 833 5.222589 GGATAAGGTAGGGAGAGGGATAAGT 60.223 48.000 0.00 0.00 0.00 2.24
827 884 2.875485 GTGCGTCGGAGCTGACTA 59.125 61.111 7.76 0.00 36.71 2.59
843 900 6.109359 AGCTGACTAATAAAGAGCGTTGATT 58.891 36.000 0.00 0.00 31.80 2.57
844 901 6.595716 AGCTGACTAATAAAGAGCGTTGATTT 59.404 34.615 0.00 0.00 31.80 2.17
845 902 7.119846 AGCTGACTAATAAAGAGCGTTGATTTT 59.880 33.333 0.00 0.00 31.80 1.82
846 903 8.388103 GCTGACTAATAAAGAGCGTTGATTTTA 58.612 33.333 0.00 0.00 0.00 1.52
856 913 7.637709 AGAGCGTTGATTTTAAACAATTTCC 57.362 32.000 0.00 0.00 0.00 3.13
932 990 8.133024 AGGGATATTCTCTTGCTAGTATTCTG 57.867 38.462 0.00 0.00 0.00 3.02
1037 1095 4.537135 TTCCACTCTCATTTAAGAGCGT 57.463 40.909 0.92 0.00 45.56 5.07
1061 1119 7.527457 GTGAATACAAGGAGGTATTTTGTGTC 58.473 38.462 0.00 0.00 42.43 3.67
1068 1126 4.292306 AGGAGGTATTTTGTGTCTGGGAAT 59.708 41.667 0.00 0.00 0.00 3.01
1073 1131 3.304911 TTTTGTGTCTGGGAATGTCCA 57.695 42.857 0.00 0.00 38.64 4.02
1220 1341 9.882996 AACATGTATATGCTATTTTCAATCGTG 57.117 29.630 0.00 0.00 37.85 4.35
1237 1358 9.942850 TTCAATCGTGTCATGGATATTATATGT 57.057 29.630 0.00 0.00 0.00 2.29
1386 1508 4.929819 TGGGTAAAAGCCAAGAAGTTTC 57.070 40.909 0.00 0.00 43.74 2.78
1451 3837 7.847096 TCTTCTACATTGAATGGTAGCTACAA 58.153 34.615 24.75 15.26 37.49 2.41
1544 3950 7.587375 ACCTAACCACCTAACCCTATTTTTA 57.413 36.000 0.00 0.00 0.00 1.52
1664 4075 5.714806 CCATGTGGTAAGGAAAAACTGGTAT 59.285 40.000 0.00 0.00 0.00 2.73
1766 4181 8.690203 TGTTTCACTCTTTATCTTTGGATTCA 57.310 30.769 0.00 0.00 33.71 2.57
1781 4196 7.939039 TCTTTGGATTCATATCTAATGACCCAC 59.061 37.037 7.44 0.00 33.45 4.61
1786 4201 3.887110 TCATATCTAATGACCCACGACGT 59.113 43.478 0.00 0.00 0.00 4.34
1802 4217 1.028330 ACGTAATCCTGGACGCGAGA 61.028 55.000 15.93 1.05 42.81 4.04
1815 4230 4.512198 TGGACGCGAGAAGTAAAAATTCAA 59.488 37.500 15.93 0.00 0.00 2.69
1896 4312 6.127619 GGGTCAGAATTCTTTCCAATTCGAAT 60.128 38.462 20.53 4.39 44.40 3.34
1934 4350 2.421248 GGGAGCAGAAAGAGAGGGATTG 60.421 54.545 0.00 0.00 0.00 2.67
1938 4354 3.526841 AGCAGAAAGAGAGGGATTGGAAT 59.473 43.478 0.00 0.00 0.00 3.01
2006 4423 1.039785 TCCACTCAGCCATCTCTCCG 61.040 60.000 0.00 0.00 0.00 4.63
2011 4428 0.976641 TCAGCCATCTCTCCGTGTTT 59.023 50.000 0.00 0.00 0.00 2.83
2023 4440 2.281517 TCCGTGTTTCAAAGCGAAAGA 58.718 42.857 0.00 0.00 44.26 2.52
2026 4443 3.664025 CCGTGTTTCAAAGCGAAAGATTC 59.336 43.478 0.00 0.00 44.26 2.52
2047 4464 6.560003 TTCCCGTGATATGATATAGGCAAT 57.440 37.500 0.00 0.00 0.00 3.56
2074 4493 5.590104 AAGAAATAATGGTTGCAAAACGC 57.410 34.783 0.00 0.00 35.09 4.84
2075 4494 3.993736 AGAAATAATGGTTGCAAAACGCC 59.006 39.130 0.00 0.00 35.09 5.68
2174 4594 9.812347 ATTTCTTGCCTATATGATATCACCAAA 57.188 29.630 7.78 0.00 0.00 3.28
2175 4595 8.621532 TTCTTGCCTATATGATATCACCAAAC 57.378 34.615 7.78 0.00 0.00 2.93
2176 4596 7.977818 TCTTGCCTATATGATATCACCAAACT 58.022 34.615 7.78 0.00 0.00 2.66
2177 4597 8.439971 TCTTGCCTATATGATATCACCAAACTT 58.560 33.333 7.78 0.00 0.00 2.66
2178 4598 9.725019 CTTGCCTATATGATATCACCAAACTTA 57.275 33.333 7.78 0.00 0.00 2.24
2193 4613 9.906660 TCACCAAACTTAAAGCAATTAACATAG 57.093 29.630 0.00 0.00 30.42 2.23
2194 4614 8.647226 CACCAAACTTAAAGCAATTAACATAGC 58.353 33.333 0.00 0.00 30.42 2.97
2195 4615 8.364142 ACCAAACTTAAAGCAATTAACATAGCA 58.636 29.630 0.00 0.00 30.42 3.49
2196 4616 8.647226 CCAAACTTAAAGCAATTAACATAGCAC 58.353 33.333 0.00 0.00 30.42 4.40
2197 4617 8.647226 CAAACTTAAAGCAATTAACATAGCACC 58.353 33.333 0.00 0.00 30.42 5.01
2198 4618 7.461182 ACTTAAAGCAATTAACATAGCACCA 57.539 32.000 0.00 0.00 30.42 4.17
2199 4619 7.891561 ACTTAAAGCAATTAACATAGCACCAA 58.108 30.769 0.00 0.00 30.42 3.67
2200 4620 8.364142 ACTTAAAGCAATTAACATAGCACCAAA 58.636 29.630 0.00 0.00 30.42 3.28
2201 4621 8.527567 TTAAAGCAATTAACATAGCACCAAAC 57.472 30.769 0.00 0.00 0.00 2.93
2202 4622 5.982890 AGCAATTAACATAGCACCAAACT 57.017 34.783 0.00 0.00 0.00 2.66
2203 4623 6.345096 AGCAATTAACATAGCACCAAACTT 57.655 33.333 0.00 0.00 0.00 2.66
2204 4624 7.461182 AGCAATTAACATAGCACCAAACTTA 57.539 32.000 0.00 0.00 0.00 2.24
2205 4625 7.891561 AGCAATTAACATAGCACCAAACTTAA 58.108 30.769 0.00 0.00 0.00 1.85
2206 4626 8.364142 AGCAATTAACATAGCACCAAACTTAAA 58.636 29.630 0.00 0.00 0.00 1.52
2207 4627 8.647226 GCAATTAACATAGCACCAAACTTAAAG 58.353 33.333 0.00 0.00 0.00 1.85
2208 4628 9.906660 CAATTAACATAGCACCAAACTTAAAGA 57.093 29.630 0.00 0.00 0.00 2.52
2212 4632 6.970484 ACATAGCACCAAACTTAAAGAAGTG 58.030 36.000 0.00 0.00 45.50 3.16
2213 4633 4.307443 AGCACCAAACTTAAAGAAGTGC 57.693 40.909 4.14 4.14 45.50 4.40
2214 4634 3.381045 GCACCAAACTTAAAGAAGTGCC 58.619 45.455 0.00 0.00 45.50 5.01
2215 4635 3.798889 GCACCAAACTTAAAGAAGTGCCC 60.799 47.826 0.00 0.00 45.50 5.36
2216 4636 3.383185 CACCAAACTTAAAGAAGTGCCCA 59.617 43.478 0.00 0.00 45.50 5.36
2217 4637 3.383505 ACCAAACTTAAAGAAGTGCCCAC 59.616 43.478 0.00 0.00 45.50 4.61
2218 4638 3.383185 CCAAACTTAAAGAAGTGCCCACA 59.617 43.478 0.82 0.00 45.50 4.17
2219 4639 4.142049 CCAAACTTAAAGAAGTGCCCACAA 60.142 41.667 0.82 0.00 45.50 3.33
2220 4640 4.918810 AACTTAAAGAAGTGCCCACAAG 57.081 40.909 0.82 0.00 45.50 3.16
2221 4641 3.898482 ACTTAAAGAAGTGCCCACAAGT 58.102 40.909 0.82 0.00 44.50 3.16
2222 4642 4.278310 ACTTAAAGAAGTGCCCACAAGTT 58.722 39.130 0.82 0.00 44.50 2.66
2223 4643 4.338400 ACTTAAAGAAGTGCCCACAAGTTC 59.662 41.667 0.82 0.00 44.50 3.01
2224 4644 2.736670 AAGAAGTGCCCACAAGTTCT 57.263 45.000 0.82 0.00 34.36 3.01
2225 4645 2.736670 AGAAGTGCCCACAAGTTCTT 57.263 45.000 0.82 0.00 30.61 2.52
2226 4646 3.018423 AGAAGTGCCCACAAGTTCTTT 57.982 42.857 0.82 0.00 30.61 2.52
2227 4647 4.164843 AGAAGTGCCCACAAGTTCTTTA 57.835 40.909 0.82 0.00 30.61 1.85
2228 4648 4.532834 AGAAGTGCCCACAAGTTCTTTAA 58.467 39.130 0.82 0.00 30.61 1.52
2229 4649 5.140454 AGAAGTGCCCACAAGTTCTTTAAT 58.860 37.500 0.82 0.00 30.61 1.40
2230 4650 5.598417 AGAAGTGCCCACAAGTTCTTTAATT 59.402 36.000 0.82 0.00 30.61 1.40
2231 4651 5.869649 AGTGCCCACAAGTTCTTTAATTT 57.130 34.783 0.82 0.00 0.00 1.82
2232 4652 6.233905 AGTGCCCACAAGTTCTTTAATTTT 57.766 33.333 0.82 0.00 0.00 1.82
2233 4653 7.354751 AGTGCCCACAAGTTCTTTAATTTTA 57.645 32.000 0.82 0.00 0.00 1.52
2234 4654 7.787028 AGTGCCCACAAGTTCTTTAATTTTAA 58.213 30.769 0.82 0.00 0.00 1.52
2235 4655 7.709182 AGTGCCCACAAGTTCTTTAATTTTAAC 59.291 33.333 0.82 0.00 0.00 2.01
2236 4656 7.709182 GTGCCCACAAGTTCTTTAATTTTAACT 59.291 33.333 0.00 0.00 33.72 2.24
2237 4657 8.915036 TGCCCACAAGTTCTTTAATTTTAACTA 58.085 29.630 0.00 0.00 32.09 2.24
2238 4658 9.188588 GCCCACAAGTTCTTTAATTTTAACTAC 57.811 33.333 0.00 0.00 32.09 2.73
2248 4668 9.223099 TCTTTAATTTTAACTACACTAGCCACC 57.777 33.333 0.00 0.00 0.00 4.61
2249 4669 9.227777 CTTTAATTTTAACTACACTAGCCACCT 57.772 33.333 0.00 0.00 0.00 4.00
2250 4670 8.556213 TTAATTTTAACTACACTAGCCACCTG 57.444 34.615 0.00 0.00 0.00 4.00
2251 4671 5.811796 TTTTAACTACACTAGCCACCTGA 57.188 39.130 0.00 0.00 0.00 3.86
2252 4672 4.796038 TTAACTACACTAGCCACCTGAC 57.204 45.455 0.00 0.00 0.00 3.51
2253 4673 2.606751 ACTACACTAGCCACCTGACT 57.393 50.000 0.00 0.00 0.00 3.41
2254 4674 2.890814 ACTACACTAGCCACCTGACTT 58.109 47.619 0.00 0.00 0.00 3.01
2255 4675 2.563179 ACTACACTAGCCACCTGACTTG 59.437 50.000 0.00 0.00 0.00 3.16
2256 4676 0.035458 ACACTAGCCACCTGACTTGC 59.965 55.000 0.00 0.00 0.00 4.01
2257 4677 0.035317 CACTAGCCACCTGACTTGCA 59.965 55.000 0.00 0.00 0.00 4.08
2258 4678 0.035458 ACTAGCCACCTGACTTGCAC 59.965 55.000 0.00 0.00 0.00 4.57
2259 4679 0.674895 CTAGCCACCTGACTTGCACC 60.675 60.000 0.00 0.00 0.00 5.01
2260 4680 1.127567 TAGCCACCTGACTTGCACCT 61.128 55.000 0.00 0.00 0.00 4.00
2261 4681 1.968540 GCCACCTGACTTGCACCTC 60.969 63.158 0.00 0.00 0.00 3.85
2262 4682 1.757306 CCACCTGACTTGCACCTCT 59.243 57.895 0.00 0.00 0.00 3.69
2263 4683 0.976641 CCACCTGACTTGCACCTCTA 59.023 55.000 0.00 0.00 0.00 2.43
2264 4684 1.066573 CCACCTGACTTGCACCTCTAG 60.067 57.143 0.00 0.00 0.00 2.43
2265 4685 1.066573 CACCTGACTTGCACCTCTAGG 60.067 57.143 0.00 0.00 42.17 3.02
2266 4686 0.107945 CCTGACTTGCACCTCTAGGC 60.108 60.000 0.00 0.00 39.32 3.93
2267 4687 0.610174 CTGACTTGCACCTCTAGGCA 59.390 55.000 0.00 0.00 39.32 4.75
2268 4688 0.610174 TGACTTGCACCTCTAGGCAG 59.390 55.000 0.00 0.00 41.68 4.85
2269 4689 0.898320 GACTTGCACCTCTAGGCAGA 59.102 55.000 0.00 0.00 41.68 4.26
2270 4690 0.901124 ACTTGCACCTCTAGGCAGAG 59.099 55.000 0.00 6.90 46.85 3.35
2281 4701 2.232452 TCTAGGCAGAGACTTGAGTTGC 59.768 50.000 0.00 0.00 0.00 4.17
2282 4702 2.549332 GGCAGAGACTTGAGTTGCC 58.451 57.895 8.98 8.98 46.39 4.52
2283 4703 3.621953 GCAGAGACTTGAGTTGCCT 57.378 52.632 0.00 0.00 0.00 4.75
2284 4704 1.155042 GCAGAGACTTGAGTTGCCTG 58.845 55.000 0.00 0.00 0.00 4.85
2285 4705 1.155042 CAGAGACTTGAGTTGCCTGC 58.845 55.000 0.00 0.00 0.00 4.85
2286 4706 1.055040 AGAGACTTGAGTTGCCTGCT 58.945 50.000 0.00 0.00 0.00 4.24
2287 4707 1.419387 AGAGACTTGAGTTGCCTGCTT 59.581 47.619 0.00 0.00 0.00 3.91
2288 4708 1.534595 GAGACTTGAGTTGCCTGCTTG 59.465 52.381 0.00 0.00 0.00 4.01
2289 4709 1.133976 AGACTTGAGTTGCCTGCTTGT 60.134 47.619 0.00 0.00 0.00 3.16
2290 4710 1.678101 GACTTGAGTTGCCTGCTTGTT 59.322 47.619 0.00 0.00 0.00 2.83
2291 4711 1.678101 ACTTGAGTTGCCTGCTTGTTC 59.322 47.619 0.00 0.00 0.00 3.18
2292 4712 1.677576 CTTGAGTTGCCTGCTTGTTCA 59.322 47.619 0.00 0.00 0.00 3.18
2293 4713 1.024271 TGAGTTGCCTGCTTGTTCAC 58.976 50.000 0.00 0.00 0.00 3.18
2294 4714 0.040958 GAGTTGCCTGCTTGTTCACG 60.041 55.000 0.00 0.00 0.00 4.35
2295 4715 1.008538 GTTGCCTGCTTGTTCACGG 60.009 57.895 0.00 0.00 0.00 4.94
2296 4716 1.453015 TTGCCTGCTTGTTCACGGT 60.453 52.632 0.00 0.00 0.00 4.83
2297 4717 1.034838 TTGCCTGCTTGTTCACGGTT 61.035 50.000 0.00 0.00 0.00 4.44
2298 4718 1.008538 GCCTGCTTGTTCACGGTTG 60.009 57.895 0.00 0.00 0.00 3.77
2299 4719 1.654220 CCTGCTTGTTCACGGTTGG 59.346 57.895 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.974108 AGTAGTCGCCATAAACACAATAGT 58.026 37.500 0.00 0.00 0.00 2.12
9 10 6.141844 CGTAGTAGTCGCCATAAACACAATAG 59.858 42.308 0.00 0.00 0.00 1.73
10 11 5.972973 CGTAGTAGTCGCCATAAACACAATA 59.027 40.000 0.00 0.00 0.00 1.90
11 12 4.802039 CGTAGTAGTCGCCATAAACACAAT 59.198 41.667 0.00 0.00 0.00 2.71
12 13 4.082841 TCGTAGTAGTCGCCATAAACACAA 60.083 41.667 0.00 0.00 0.00 3.33
13 14 3.439825 TCGTAGTAGTCGCCATAAACACA 59.560 43.478 0.00 0.00 0.00 3.72
14 15 4.019919 TCGTAGTAGTCGCCATAAACAC 57.980 45.455 0.00 0.00 0.00 3.32
15 16 4.700268 TTCGTAGTAGTCGCCATAAACA 57.300 40.909 0.00 0.00 0.00 2.83
16 17 5.276270 TGATTCGTAGTAGTCGCCATAAAC 58.724 41.667 0.00 0.00 0.00 2.01
17 18 5.503662 TGATTCGTAGTAGTCGCCATAAA 57.496 39.130 0.00 0.00 0.00 1.40
18 19 5.335426 GGATGATTCGTAGTAGTCGCCATAA 60.335 44.000 0.00 0.00 0.00 1.90
19 20 4.155462 GGATGATTCGTAGTAGTCGCCATA 59.845 45.833 0.00 0.00 0.00 2.74
20 21 3.057456 GGATGATTCGTAGTAGTCGCCAT 60.057 47.826 0.00 0.00 0.00 4.40
21 22 2.292569 GGATGATTCGTAGTAGTCGCCA 59.707 50.000 0.00 0.00 0.00 5.69
128 129 1.814793 GTGAGAGAAAAGGGTCAGCC 58.185 55.000 0.00 0.00 0.00 4.85
146 147 2.665185 GCTGGTTGGAAGCGTCGT 60.665 61.111 0.00 0.00 0.00 4.34
149 150 4.660938 GGGGCTGGTTGGAAGCGT 62.661 66.667 0.00 0.00 41.78 5.07
153 154 4.299796 GCAGGGGGCTGGTTGGAA 62.300 66.667 0.00 0.00 40.25 3.53
292 301 3.833645 ATTGGAGCGCTCGCCGTA 61.834 61.111 29.81 13.72 43.17 4.02
342 351 1.930908 GCTGCAATGGAGCTTCGCTT 61.931 55.000 19.55 0.00 39.88 4.68
364 395 0.813184 GCTGCATTGGAGCTTTGCTA 59.187 50.000 21.41 1.14 39.88 3.49
404 435 2.922503 TTGGAGCTCCGCCACAGA 60.923 61.111 27.43 5.35 39.43 3.41
406 437 2.616797 TTTGTTGGAGCTCCGCCACA 62.617 55.000 27.43 24.48 39.43 4.17
408 439 1.896660 GTTTGTTGGAGCTCCGCCA 60.897 57.895 27.43 22.14 39.43 5.69
497 547 4.719616 GCTTGCACCGTCGTTCGC 62.720 66.667 0.00 0.00 38.35 4.70
500 550 3.649986 GCAGCTTGCACCGTCGTT 61.650 61.111 0.00 0.00 44.26 3.85
541 593 2.354188 CTCACGTCGTTGCACCGA 60.354 61.111 0.74 0.74 33.79 4.69
565 617 0.685097 ACACCACTACAGCGAACCAT 59.315 50.000 0.00 0.00 0.00 3.55
571 623 1.540267 ACACTCTACACCACTACAGCG 59.460 52.381 0.00 0.00 0.00 5.18
576 628 0.885879 CGCCACACTCTACACCACTA 59.114 55.000 0.00 0.00 0.00 2.74
589 641 0.885879 CTACTGTCCTACACGCCACA 59.114 55.000 0.00 0.00 0.00 4.17
719 771 0.534203 TTCCCGCAGAAGGTGTTCAC 60.534 55.000 0.00 0.00 34.82 3.18
724 776 0.321671 TCTCTTTCCCGCAGAAGGTG 59.678 55.000 0.00 0.00 35.40 4.00
734 786 2.296471 TCCGCTCGATTATCTCTTTCCC 59.704 50.000 0.00 0.00 0.00 3.97
747 799 2.228059 CTACCTTATCCTTCCGCTCGA 58.772 52.381 0.00 0.00 0.00 4.04
763 815 3.117054 AGACACTTATCCCTCTCCCTACC 60.117 52.174 0.00 0.00 0.00 3.18
765 817 3.792114 TGAGACACTTATCCCTCTCCCTA 59.208 47.826 0.00 0.00 0.00 3.53
774 826 1.202818 GGCCCCATGAGACACTTATCC 60.203 57.143 0.00 0.00 0.00 2.59
779 831 2.204136 TGGGCCCCATGAGACACT 60.204 61.111 22.27 0.00 0.00 3.55
780 832 2.044946 GTGGGCCCCATGAGACAC 60.045 66.667 22.27 3.64 35.28 3.67
781 833 3.338250 GGTGGGCCCCATGAGACA 61.338 66.667 22.27 0.00 35.28 3.41
808 860 4.702081 GTCAGCTCCGACGCACGT 62.702 66.667 0.00 0.00 40.78 4.49
811 868 1.385528 TATTAGTCAGCTCCGACGCA 58.614 50.000 0.00 0.00 40.98 5.24
1030 1088 2.567615 ACCTCCTTGTATTCACGCTCTT 59.432 45.455 0.00 0.00 0.00 2.85
1035 1093 6.148811 ACACAAAATACCTCCTTGTATTCACG 59.851 38.462 0.00 0.00 39.81 4.35
1037 1095 7.390440 CAGACACAAAATACCTCCTTGTATTCA 59.610 37.037 0.00 0.00 39.81 2.57
1144 1205 8.038492 AGCATTTCATTCTTTCTTGTAGAGTC 57.962 34.615 0.00 0.00 0.00 3.36
1157 1218 5.927281 AGGCATAACAAGCATTTCATTCT 57.073 34.783 0.00 0.00 0.00 2.40
1158 1219 9.918630 ATATTAGGCATAACAAGCATTTCATTC 57.081 29.630 0.00 0.00 0.00 2.67
1197 1258 9.271828 TGACACGATTGAAAATAGCATATACAT 57.728 29.630 0.00 0.00 0.00 2.29
1270 1391 2.985957 ACAACAGCTTGCCAAACAAT 57.014 40.000 0.00 0.00 37.72 2.71
1451 3837 7.486407 AGAAAGGCTGATCCAAATTTATTGT 57.514 32.000 0.00 0.00 37.29 2.71
1642 4053 7.238710 AGAATACCAGTTTTTCCTTACCACAT 58.761 34.615 0.00 0.00 0.00 3.21
1766 4181 6.349944 GGATTACGTCGTGGGTCATTAGATAT 60.350 42.308 8.47 0.00 0.00 1.63
1781 4196 1.937846 CGCGTCCAGGATTACGTCG 60.938 63.158 0.00 0.00 41.10 5.12
1786 4201 1.471119 ACTTCTCGCGTCCAGGATTA 58.529 50.000 5.77 0.00 0.00 1.75
1869 4285 4.682021 ATTGGAAAGAATTCTGACCCCT 57.318 40.909 21.01 10.62 35.79 4.79
1896 4312 1.999295 TCCCTTGGATCATTTGGGACA 59.001 47.619 9.90 0.00 41.57 4.02
1934 4350 6.521162 ACAATTGTTTTGTACCAAGGATTCC 58.479 36.000 4.92 0.00 0.00 3.01
2006 4423 3.981416 GGGAATCTTTCGCTTTGAAACAC 59.019 43.478 0.00 0.00 41.59 3.32
2011 4428 1.804151 CACGGGAATCTTTCGCTTTGA 59.196 47.619 3.33 0.00 40.15 2.69
2023 4440 6.560003 TTGCCTATATCATATCACGGGAAT 57.440 37.500 0.00 0.00 0.00 3.01
2026 4443 8.908786 ATTTATTGCCTATATCATATCACGGG 57.091 34.615 0.00 0.00 0.00 5.28
2149 4569 9.066892 GTTTGGTGATATCATATAGGCAAGAAA 57.933 33.333 9.02 0.00 0.00 2.52
2150 4570 8.439971 AGTTTGGTGATATCATATAGGCAAGAA 58.560 33.333 9.02 0.00 0.00 2.52
2151 4571 7.977818 AGTTTGGTGATATCATATAGGCAAGA 58.022 34.615 9.02 0.00 0.00 3.02
2152 4572 8.627208 AAGTTTGGTGATATCATATAGGCAAG 57.373 34.615 9.02 0.00 0.00 4.01
2167 4587 9.906660 CTATGTTAATTGCTTTAAGTTTGGTGA 57.093 29.630 0.00 0.00 30.46 4.02
2168 4588 8.647226 GCTATGTTAATTGCTTTAAGTTTGGTG 58.353 33.333 0.00 0.00 32.54 4.17
2169 4589 8.364142 TGCTATGTTAATTGCTTTAAGTTTGGT 58.636 29.630 0.00 0.00 35.79 3.67
2170 4590 8.647226 GTGCTATGTTAATTGCTTTAAGTTTGG 58.353 33.333 0.00 0.00 35.79 3.28
2171 4591 8.647226 GGTGCTATGTTAATTGCTTTAAGTTTG 58.353 33.333 0.00 0.00 35.79 2.93
2172 4592 8.364142 TGGTGCTATGTTAATTGCTTTAAGTTT 58.636 29.630 0.00 0.00 35.79 2.66
2173 4593 7.891561 TGGTGCTATGTTAATTGCTTTAAGTT 58.108 30.769 0.00 0.00 35.79 2.66
2174 4594 7.461182 TGGTGCTATGTTAATTGCTTTAAGT 57.539 32.000 0.00 0.00 35.79 2.24
2175 4595 8.647226 GTTTGGTGCTATGTTAATTGCTTTAAG 58.353 33.333 0.00 0.00 35.79 1.85
2176 4596 8.364142 AGTTTGGTGCTATGTTAATTGCTTTAA 58.636 29.630 0.00 0.00 35.79 1.52
2177 4597 7.891561 AGTTTGGTGCTATGTTAATTGCTTTA 58.108 30.769 0.00 0.00 35.79 1.85
2178 4598 6.758254 AGTTTGGTGCTATGTTAATTGCTTT 58.242 32.000 0.00 0.00 35.79 3.51
2179 4599 6.345096 AGTTTGGTGCTATGTTAATTGCTT 57.655 33.333 0.00 0.00 35.79 3.91
2180 4600 5.982890 AGTTTGGTGCTATGTTAATTGCT 57.017 34.783 0.00 0.00 35.79 3.91
2181 4601 8.527567 TTTAAGTTTGGTGCTATGTTAATTGC 57.472 30.769 0.00 0.00 35.40 3.56
2182 4602 9.906660 TCTTTAAGTTTGGTGCTATGTTAATTG 57.093 29.630 0.00 0.00 0.00 2.32
2185 4605 9.127277 ACTTCTTTAAGTTTGGTGCTATGTTAA 57.873 29.630 0.00 0.00 43.60 2.01
2186 4606 8.564574 CACTTCTTTAAGTTTGGTGCTATGTTA 58.435 33.333 0.00 0.00 43.60 2.41
2187 4607 7.425606 CACTTCTTTAAGTTTGGTGCTATGTT 58.574 34.615 0.00 0.00 43.60 2.71
2188 4608 6.515035 GCACTTCTTTAAGTTTGGTGCTATGT 60.515 38.462 18.10 0.00 43.60 2.29
2189 4609 5.858581 GCACTTCTTTAAGTTTGGTGCTATG 59.141 40.000 18.10 0.00 43.60 2.23
2190 4610 5.048013 GGCACTTCTTTAAGTTTGGTGCTAT 60.048 40.000 21.38 0.00 43.60 2.97
2191 4611 4.277423 GGCACTTCTTTAAGTTTGGTGCTA 59.723 41.667 21.38 0.00 43.60 3.49
2192 4612 3.068165 GGCACTTCTTTAAGTTTGGTGCT 59.932 43.478 21.38 0.00 43.60 4.40
2193 4613 3.381045 GGCACTTCTTTAAGTTTGGTGC 58.619 45.455 17.59 17.59 43.60 5.01
2194 4614 3.383185 TGGGCACTTCTTTAAGTTTGGTG 59.617 43.478 0.00 0.00 43.60 4.17
2195 4615 3.383505 GTGGGCACTTCTTTAAGTTTGGT 59.616 43.478 0.00 0.00 43.60 3.67
2196 4616 3.383185 TGTGGGCACTTCTTTAAGTTTGG 59.617 43.478 0.00 0.00 43.60 3.28
2197 4617 4.647424 TGTGGGCACTTCTTTAAGTTTG 57.353 40.909 0.00 0.00 43.60 2.93
2198 4618 4.709886 ACTTGTGGGCACTTCTTTAAGTTT 59.290 37.500 0.00 0.00 43.60 2.66
2199 4619 4.278310 ACTTGTGGGCACTTCTTTAAGTT 58.722 39.130 0.00 0.00 43.60 2.66
2201 4621 4.580580 AGAACTTGTGGGCACTTCTTTAAG 59.419 41.667 0.00 0.00 38.77 1.85
2202 4622 4.532834 AGAACTTGTGGGCACTTCTTTAA 58.467 39.130 0.00 0.00 0.00 1.52
2203 4623 4.164843 AGAACTTGTGGGCACTTCTTTA 57.835 40.909 0.00 0.00 0.00 1.85
2204 4624 3.018423 AGAACTTGTGGGCACTTCTTT 57.982 42.857 0.00 0.00 0.00 2.52
2205 4625 2.736670 AGAACTTGTGGGCACTTCTT 57.263 45.000 0.00 0.00 0.00 2.52
2206 4626 2.736670 AAGAACTTGTGGGCACTTCT 57.263 45.000 0.00 0.00 0.00 2.85
2207 4627 4.911514 TTAAAGAACTTGTGGGCACTTC 57.088 40.909 0.00 0.00 0.00 3.01
2208 4628 5.869649 AATTAAAGAACTTGTGGGCACTT 57.130 34.783 0.00 0.00 0.00 3.16
2209 4629 5.869649 AAATTAAAGAACTTGTGGGCACT 57.130 34.783 0.00 0.00 0.00 4.40
2210 4630 7.709182 AGTTAAAATTAAAGAACTTGTGGGCAC 59.291 33.333 0.00 0.00 0.00 5.01
2211 4631 7.787028 AGTTAAAATTAAAGAACTTGTGGGCA 58.213 30.769 0.00 0.00 0.00 5.36
2212 4632 9.188588 GTAGTTAAAATTAAAGAACTTGTGGGC 57.811 33.333 0.00 0.00 34.15 5.36
2222 4642 9.223099 GGTGGCTAGTGTAGTTAAAATTAAAGA 57.777 33.333 0.00 0.00 0.00 2.52
2223 4643 9.227777 AGGTGGCTAGTGTAGTTAAAATTAAAG 57.772 33.333 0.00 0.00 0.00 1.85
2224 4644 9.005777 CAGGTGGCTAGTGTAGTTAAAATTAAA 57.994 33.333 0.00 0.00 0.00 1.52
2225 4645 8.377034 TCAGGTGGCTAGTGTAGTTAAAATTAA 58.623 33.333 0.00 0.00 0.00 1.40
2226 4646 7.820872 GTCAGGTGGCTAGTGTAGTTAAAATTA 59.179 37.037 0.00 0.00 0.00 1.40
2227 4647 6.653740 GTCAGGTGGCTAGTGTAGTTAAAATT 59.346 38.462 0.00 0.00 0.00 1.82
2228 4648 6.013639 AGTCAGGTGGCTAGTGTAGTTAAAAT 60.014 38.462 0.00 0.00 0.00 1.82
2229 4649 5.306160 AGTCAGGTGGCTAGTGTAGTTAAAA 59.694 40.000 0.00 0.00 0.00 1.52
2230 4650 4.836736 AGTCAGGTGGCTAGTGTAGTTAAA 59.163 41.667 0.00 0.00 0.00 1.52
2231 4651 4.413760 AGTCAGGTGGCTAGTGTAGTTAA 58.586 43.478 0.00 0.00 0.00 2.01
2232 4652 4.043608 AGTCAGGTGGCTAGTGTAGTTA 57.956 45.455 0.00 0.00 0.00 2.24
2233 4653 2.890814 AGTCAGGTGGCTAGTGTAGTT 58.109 47.619 0.00 0.00 0.00 2.24
2234 4654 2.563179 CAAGTCAGGTGGCTAGTGTAGT 59.437 50.000 0.00 0.00 0.00 2.73
2235 4655 2.675317 GCAAGTCAGGTGGCTAGTGTAG 60.675 54.545 0.00 0.00 0.00 2.74
2236 4656 1.275291 GCAAGTCAGGTGGCTAGTGTA 59.725 52.381 0.00 0.00 0.00 2.90
2237 4657 0.035458 GCAAGTCAGGTGGCTAGTGT 59.965 55.000 0.00 0.00 0.00 3.55
2238 4658 0.035317 TGCAAGTCAGGTGGCTAGTG 59.965 55.000 0.00 0.00 0.00 2.74
2239 4659 0.035458 GTGCAAGTCAGGTGGCTAGT 59.965 55.000 0.00 0.00 0.00 2.57
2240 4660 0.674895 GGTGCAAGTCAGGTGGCTAG 60.675 60.000 0.00 0.00 0.00 3.42
2241 4661 1.127567 AGGTGCAAGTCAGGTGGCTA 61.128 55.000 0.00 0.00 0.00 3.93
2242 4662 2.113986 GGTGCAAGTCAGGTGGCT 59.886 61.111 0.00 0.00 0.00 4.75
2243 4663 1.968540 GAGGTGCAAGTCAGGTGGC 60.969 63.158 0.00 0.00 0.00 5.01
2244 4664 0.976641 TAGAGGTGCAAGTCAGGTGG 59.023 55.000 0.00 0.00 0.00 4.61
2245 4665 1.066573 CCTAGAGGTGCAAGTCAGGTG 60.067 57.143 0.00 0.00 0.00 4.00
2246 4666 1.270907 CCTAGAGGTGCAAGTCAGGT 58.729 55.000 0.00 0.00 0.00 4.00
2247 4667 0.107945 GCCTAGAGGTGCAAGTCAGG 60.108 60.000 0.00 0.00 37.57 3.86
2248 4668 0.610174 TGCCTAGAGGTGCAAGTCAG 59.390 55.000 0.00 0.00 37.57 3.51
2249 4669 0.610174 CTGCCTAGAGGTGCAAGTCA 59.390 55.000 0.00 0.00 36.98 3.41
2250 4670 0.898320 TCTGCCTAGAGGTGCAAGTC 59.102 55.000 0.00 0.00 36.98 3.01
2251 4671 0.901124 CTCTGCCTAGAGGTGCAAGT 59.099 55.000 0.00 0.00 45.47 3.16
2252 4672 3.756739 CTCTGCCTAGAGGTGCAAG 57.243 57.895 0.00 0.00 45.47 4.01
2260 4680 2.232452 GCAACTCAAGTCTCTGCCTAGA 59.768 50.000 0.00 0.00 0.00 2.43
2261 4681 2.615869 GCAACTCAAGTCTCTGCCTAG 58.384 52.381 0.00 0.00 0.00 3.02
2262 4682 1.276421 GGCAACTCAAGTCTCTGCCTA 59.724 52.381 14.36 0.00 42.92 3.93
2263 4683 0.036022 GGCAACTCAAGTCTCTGCCT 59.964 55.000 14.36 0.00 42.92 4.75
2264 4684 2.549332 GGCAACTCAAGTCTCTGCC 58.451 57.895 8.22 8.22 40.78 4.85
2277 4697 1.008538 CCGTGAACAAGCAGGCAAC 60.009 57.895 0.00 0.00 0.00 4.17
2278 4698 1.034838 AACCGTGAACAAGCAGGCAA 61.035 50.000 0.00 0.00 0.00 4.52
2279 4699 1.453015 AACCGTGAACAAGCAGGCA 60.453 52.632 0.00 0.00 0.00 4.75
2280 4700 1.008538 CAACCGTGAACAAGCAGGC 60.009 57.895 0.00 0.00 0.00 4.85
2281 4701 1.654220 CCAACCGTGAACAAGCAGG 59.346 57.895 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.