Multiple sequence alignment - TraesCS3B01G293100

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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 TraesCS3B01G293100 chr3B 100.000 5355 0 0 1 5355 472117092 472111738 0.000000e+00 9889.0
1 TraesCS3B01G293100 chr3B 90.500 200 18 1 1693 1892 651678826 651678628 4.110000e-66 263.0
2 TraesCS3B01G293100 chr3A 92.640 5394 258 53 13 5345 482407661 482402346 0.000000e+00 7633.0
3 TraesCS3B01G293100 chr3A 91.626 203 16 1 1690 1892 17310870 17311071 4.080000e-71 279.0
4 TraesCS3B01G293100 chr3D 94.511 4901 171 32 13 4862 362202838 362197985 0.000000e+00 7470.0
5 TraesCS3B01G293100 chr3D 85.266 414 31 8 4770 5173 362197985 362197592 3.000000e-107 399.0
6 TraesCS3B01G293100 chr1A 90.270 185 17 1 1690 1874 521035887 521036070 1.930000e-59 241.0
7 TraesCS3B01G293100 chr1A 88.608 79 9 0 1597 1675 402803169 402803091 4.410000e-16 97.1
8 TraesCS3B01G293100 chr4B 87.685 203 18 4 1690 1892 201717448 201717253 4.170000e-56 230.0
9 TraesCS3B01G293100 chr5B 89.216 102 10 1 1584 1685 698949415 698949315 5.630000e-25 126.0
10 TraesCS3B01G293100 chr5B 93.333 45 1 2 4940 4983 581712840 581712883 1.240000e-06 65.8
11 TraesCS3B01G293100 chr5B 97.059 34 1 0 3141 3174 416545703 416545670 2.080000e-04 58.4
12 TraesCS3B01G293100 chr1D 87.342 79 10 0 1597 1675 320400163 320400241 2.050000e-14 91.6
13 TraesCS3B01G293100 chr1B 87.342 79 10 0 1597 1675 433436059 433436137 2.050000e-14 91.6
14 TraesCS3B01G293100 chr5D 91.667 48 3 1 4940 4987 474714992 474714946 1.240000e-06 65.8


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 TraesCS3B01G293100 chr3B 472111738 472117092 5354 True 9889.0 9889 100.0000 1 5355 1 chr3B.!!$R1 5354
1 TraesCS3B01G293100 chr3A 482402346 482407661 5315 True 7633.0 7633 92.6400 13 5345 1 chr3A.!!$R1 5332
2 TraesCS3B01G293100 chr3D 362197592 362202838 5246 True 3934.5 7470 89.8885 13 5173 2 chr3D.!!$R1 5160

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
552 561 0.665068 TGGTAGTGCGTAGTTGCGTG 60.665 55.000 0.00 0.00 37.81 5.34 F
2015 2055 1.732259 GGTACAGGAATTGTGCACGAG 59.268 52.381 13.31 0.69 43.39 4.18 F
2691 2735 0.035036 AGATGGCATCTGCATCTCCG 59.965 55.000 28.33 0.00 44.36 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2497 2541 0.317160 CATATCGCCAAGACGCCCTA 59.683 55.000 0.00 0.0 0.0 3.53 R
3281 3327 2.502142 TGGAGTCCGAGCTAACAGTA 57.498 50.000 4.30 0.0 0.0 2.74 R
4407 4469 1.961394 ACATATGCGACCACCTACGAT 59.039 47.619 1.58 0.0 0.0 3.73 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
58 60 5.406477 AGTTACCGTGAACGAATTTTACTCC 59.594 40.000 4.03 0.00 43.02 3.85
77 80 9.936759 TTTACTCCTTTTTGTTGTTGAGAAAAT 57.063 25.926 0.00 0.00 31.46 1.82
236 243 1.066502 TGATTTCTTCGATCGCCACCA 60.067 47.619 11.09 0.00 0.00 4.17
244 251 1.745489 GATCGCCACCACCCAGTTC 60.745 63.158 0.00 0.00 0.00 3.01
310 318 2.223144 CGAATCTGTCGGCAACTTTTCA 59.777 45.455 0.00 0.00 46.45 2.69
328 336 1.007336 CACGTCGTTCTACAGGTGGC 61.007 60.000 0.00 0.00 0.00 5.01
347 356 1.371267 GGCAAGGTTTTTCGCGACC 60.371 57.895 9.15 7.61 36.15 4.79
392 401 2.034879 ACCTCTGATTTGTGCCGCG 61.035 57.895 0.00 0.00 0.00 6.46
444 453 2.827051 CGATGCGGGGCTGATTGTG 61.827 63.158 0.00 0.00 0.00 3.33
468 477 3.390135 CAGCGTTTCTGTTCTGGAGTTA 58.610 45.455 0.00 0.00 38.02 2.24
488 497 5.470777 AGTTAGTCTCATCTACGCCATAGAC 59.529 44.000 0.00 0.00 42.90 2.59
552 561 0.665068 TGGTAGTGCGTAGTTGCGTG 60.665 55.000 0.00 0.00 37.81 5.34
581 591 7.918076 AGATTGGACAATTTTCCTACTACTGA 58.082 34.615 11.83 0.00 36.51 3.41
597 607 4.889995 ACTACTGATGACCATTGAGATCGA 59.110 41.667 0.00 0.00 0.00 3.59
627 637 4.403432 CCTTTTGGGTATCATGCTCATGTT 59.597 41.667 9.41 4.54 36.70 2.71
634 644 7.744733 TGGGTATCATGCTCATGTTAGATTTA 58.255 34.615 9.41 0.00 39.72 1.40
775 785 7.306457 CGCACTCTGATTCTGATAGTTGTATTG 60.306 40.741 0.00 0.00 0.00 1.90
804 814 6.524101 TCTGTAGTTAAATGGGCAAAATCC 57.476 37.500 0.00 0.00 0.00 3.01
888 924 3.376859 TGTCAATTACTTAGGCGGCAATG 59.623 43.478 13.08 2.38 0.00 2.82
894 930 5.744666 TTACTTAGGCGGCAATGTTATTC 57.255 39.130 13.08 0.00 0.00 1.75
966 1005 8.543774 CATTCTAGCTAGTAGTATGTTTTGCAC 58.456 37.037 20.10 0.00 33.76 4.57
1187 1226 3.591196 TGTGGCTTTGGCAATTATGTC 57.409 42.857 0.00 0.00 40.46 3.06
1222 1261 6.538742 GGCTATAGCACAAACTGATGAAGTTA 59.461 38.462 25.53 0.00 45.28 2.24
1318 1357 9.277565 CACATCTCATTGTAAGGAATTAAAACG 57.722 33.333 0.00 0.00 0.00 3.60
1320 1359 7.385778 TCTCATTGTAAGGAATTAAAACGGG 57.614 36.000 0.00 0.00 0.00 5.28
1457 1496 8.485392 TCTGTCATGGTCATGTAGAATATTTCA 58.515 33.333 10.32 0.00 39.72 2.69
1474 1513 3.616956 TTCACTGTCCTATGAGGCTTG 57.383 47.619 0.00 0.00 34.61 4.01
1487 1526 6.259608 CCTATGAGGCTTGTACTCAGAATTTG 59.740 42.308 0.00 0.00 46.98 2.32
1508 1548 7.391148 TTTGTGATAGAAGCCTTATTGTTCC 57.609 36.000 0.00 0.00 0.00 3.62
1639 1679 2.288334 TGATGATGCAATTTATGGCCGC 60.288 45.455 0.00 0.00 0.00 6.53
1657 1697 2.483876 CGCGATGGGTATGACTTTGAT 58.516 47.619 0.00 0.00 0.00 2.57
1680 1720 1.904990 TACAGGCTGCGGGTATGCAA 61.905 55.000 15.89 0.00 45.74 4.08
1799 1839 5.163642 TGGAAGAGCTCAATCTTACTCGTAC 60.164 44.000 17.77 0.00 40.31 3.67
1874 1914 4.100498 TCTGAGTTCCGAGGTTTGTACTTT 59.900 41.667 0.00 0.00 0.00 2.66
1928 1968 8.526147 TCTGGATTGGAATTCTCATTTTTCTTC 58.474 33.333 5.23 0.00 0.00 2.87
1937 1977 8.585189 AATTCTCATTTTTCTTCTCTTGTTGC 57.415 30.769 0.00 0.00 0.00 4.17
2015 2055 1.732259 GGTACAGGAATTGTGCACGAG 59.268 52.381 13.31 0.69 43.39 4.18
2050 2090 9.985730 ATACATTTTGAGTTTGATGTTCATTGT 57.014 25.926 0.00 0.00 34.76 2.71
2211 2252 9.803315 TCCAATTATATCGACATTATAGCAGTC 57.197 33.333 0.00 0.00 0.00 3.51
2416 2457 3.452755 TGCGGTAGGTTGTCATATCAG 57.547 47.619 0.00 0.00 0.00 2.90
2417 2458 2.764010 TGCGGTAGGTTGTCATATCAGT 59.236 45.455 0.00 0.00 0.00 3.41
2453 2497 7.323656 CGCTTTTTAGTGATAAAGTTCTTGTGG 59.676 37.037 0.00 0.00 34.59 4.17
2503 2547 2.663826 GAGGATCTGCTAATAGGGCG 57.336 55.000 0.00 0.00 0.00 6.13
2504 2548 1.896465 GAGGATCTGCTAATAGGGCGT 59.104 52.381 0.00 0.00 0.00 5.68
2514 2558 1.045407 AATAGGGCGTCTTGGCGATA 58.955 50.000 0.00 0.00 46.04 2.92
2527 2571 2.088423 TGGCGATATGTGGTTTGTTCC 58.912 47.619 0.00 0.00 0.00 3.62
2561 2605 9.080097 GTTGGTATATACCTCTCTTATCACTGT 57.920 37.037 28.12 0.00 46.58 3.55
2646 2690 5.431179 TCAGGGTATGGGTTTACTTCTTC 57.569 43.478 0.00 0.00 0.00 2.87
2660 2704 9.274206 GGTTTACTTCTTCTTCACTGATAGTTT 57.726 33.333 0.00 0.00 0.00 2.66
2687 2731 5.178996 CAGTAGTTAAGATGGCATCTGCATC 59.821 44.000 29.43 18.88 44.36 3.91
2691 2735 0.035036 AGATGGCATCTGCATCTCCG 59.965 55.000 28.33 0.00 44.36 4.63
2835 2879 9.774742 CAGGTATCTTAAATTTCTTTCTTTCGG 57.225 33.333 0.00 0.00 0.00 4.30
3114 3159 8.973182 TGGTTACAAAAACAGAAATAGGTCTTT 58.027 29.630 0.00 0.00 0.00 2.52
3152 3198 9.871238 TTGATGTCTACCTCTGTTTCTAAATAC 57.129 33.333 0.00 0.00 0.00 1.89
3194 3240 9.947669 TTTAAATTGAAATGCCAAAATGACTTG 57.052 25.926 0.00 0.00 0.00 3.16
3511 3568 2.613977 CCAGTGAGCAACAAGTCCTAGG 60.614 54.545 0.82 0.82 0.00 3.02
3624 3682 5.418840 TCACTAAAAGGCCCTCATTTTCATC 59.581 40.000 0.00 0.00 31.41 2.92
3738 3797 4.953940 TGCTAAGAGGTTGGCAATTTTT 57.046 36.364 1.92 0.00 46.20 1.94
3853 3913 2.880443 AGAGGTTGGCATGACAAATGT 58.120 42.857 17.49 3.33 31.17 2.71
4014 4074 2.771943 GAGGATGGGTATGGTTGTCAGA 59.228 50.000 0.00 0.00 0.00 3.27
4044 4104 5.061920 TGGTGTTAATTTTGGATTACGCC 57.938 39.130 0.00 0.00 0.00 5.68
4093 4153 2.762887 TGAAACATTTTGCAGGTCACCA 59.237 40.909 0.00 0.00 0.00 4.17
4117 4177 2.808919 AGATCTCGGTCTCCTGTTTCA 58.191 47.619 0.00 0.00 0.00 2.69
4119 4179 3.772025 AGATCTCGGTCTCCTGTTTCATT 59.228 43.478 0.00 0.00 0.00 2.57
4138 4198 5.789521 TCATTGGTAAGTCTCGACAATCAA 58.210 37.500 0.00 0.97 30.00 2.57
4141 4201 8.038351 TCATTGGTAAGTCTCGACAATCAATTA 58.962 33.333 7.68 0.82 31.92 1.40
4289 4350 0.459411 GCACTCTCTCGCCTCTTTCC 60.459 60.000 0.00 0.00 0.00 3.13
4290 4351 0.174617 CACTCTCTCGCCTCTTTCCC 59.825 60.000 0.00 0.00 0.00 3.97
4313 4374 7.226720 TCCCAGAAATCGCTTATGATTAACTTC 59.773 37.037 0.00 0.00 37.59 3.01
4356 4417 1.412710 GCAGGTGAGGTCGGATTGATA 59.587 52.381 0.00 0.00 0.00 2.15
4396 4458 3.093057 AGCGAGTGACTACTTCAGGATT 58.907 45.455 0.00 0.00 37.25 3.01
4399 4461 3.367395 CGAGTGACTACTTCAGGATTGCA 60.367 47.826 0.00 0.00 37.25 4.08
4407 4469 6.711277 ACTACTTCAGGATTGCAAGTATTCA 58.289 36.000 4.94 0.00 33.26 2.57
4419 4481 3.802685 GCAAGTATTCATCGTAGGTGGTC 59.197 47.826 0.00 0.00 0.00 4.02
4427 4489 1.395635 TCGTAGGTGGTCGCATATGT 58.604 50.000 4.29 0.00 0.00 2.29
4429 4491 2.124903 CGTAGGTGGTCGCATATGTTC 58.875 52.381 4.29 0.00 0.00 3.18
4438 4500 5.119279 GTGGTCGCATATGTTCTATCATGTC 59.881 44.000 4.29 0.00 0.00 3.06
4444 4506 5.646793 GCATATGTTCTATCATGTCCTGCAT 59.353 40.000 4.29 0.00 38.60 3.96
4537 4599 8.410673 TCTGTTCTCAGATTTAGAGTTGTACT 57.589 34.615 0.00 0.00 44.58 2.73
4538 4600 8.861086 TCTGTTCTCAGATTTAGAGTTGTACTT 58.139 33.333 0.00 0.00 44.58 2.24
4539 4601 8.818141 TGTTCTCAGATTTAGAGTTGTACTTG 57.182 34.615 0.00 0.00 34.73 3.16
4540 4602 8.421784 TGTTCTCAGATTTAGAGTTGTACTTGT 58.578 33.333 0.00 0.00 34.73 3.16
4541 4603 9.909644 GTTCTCAGATTTAGAGTTGTACTTGTA 57.090 33.333 0.00 0.00 34.73 2.41
4613 4675 6.544197 TCTGCAGTTTGTGGTAACTTGAATTA 59.456 34.615 14.67 0.00 36.24 1.40
4626 4688 6.441088 AACTTGAATTAAGAGGAGACCTGT 57.559 37.500 0.00 0.00 39.76 4.00
4697 4760 3.613494 TGTTGGTAATAAGCACGGCTA 57.387 42.857 0.00 0.00 38.25 3.93
4723 4786 6.813152 GCATAGCCACATTATGTTTTTCAACT 59.187 34.615 0.00 0.00 33.58 3.16
4736 4799 2.818751 TTCAACTCCAGGTGGTTGTT 57.181 45.000 19.78 8.27 42.15 2.83
4747 4810 2.589442 GGTTGTTGTGGACGCCGA 60.589 61.111 0.00 0.00 0.00 5.54
4748 4811 1.964373 GGTTGTTGTGGACGCCGAT 60.964 57.895 0.00 0.00 0.00 4.18
4750 4813 2.612567 TTGTTGTGGACGCCGATGC 61.613 57.895 0.00 0.00 0.00 3.91
4752 4815 4.015406 TTGTGGACGCCGATGCCT 62.015 61.111 0.00 0.00 0.00 4.75
4819 4882 1.071385 GAGGTGCTCTGATGGGTATGG 59.929 57.143 0.00 0.00 0.00 2.74
4821 4884 1.202698 GGTGCTCTGATGGGTATGGTC 60.203 57.143 0.00 0.00 0.00 4.02
4869 5024 0.389391 ACATAGGCGATCGAGGTTGG 59.611 55.000 21.57 5.44 0.00 3.77
4870 5025 0.673985 CATAGGCGATCGAGGTTGGA 59.326 55.000 21.57 0.00 0.00 3.53
4872 5027 0.673985 TAGGCGATCGAGGTTGGATG 59.326 55.000 21.57 0.00 0.00 3.51
4873 5028 1.595382 GGCGATCGAGGTTGGATGG 60.595 63.158 21.57 0.00 0.00 3.51
4874 5029 1.595382 GCGATCGAGGTTGGATGGG 60.595 63.158 21.57 0.00 0.00 4.00
4876 5031 1.832912 GATCGAGGTTGGATGGGCT 59.167 57.895 0.00 0.00 0.00 5.19
4877 5032 0.250081 GATCGAGGTTGGATGGGCTC 60.250 60.000 0.00 0.00 0.00 4.70
4878 5033 0.692419 ATCGAGGTTGGATGGGCTCT 60.692 55.000 0.00 0.00 0.00 4.09
4920 5098 0.765510 GACCAACTCCCTGTGAACCT 59.234 55.000 0.00 0.00 0.00 3.50
4987 5168 8.329502 AGTTGGAAAGAATTACTAAGCCATAGT 58.670 33.333 5.26 5.26 46.62 2.12
4988 5169 9.609346 GTTGGAAAGAATTACTAAGCCATAGTA 57.391 33.333 3.51 3.51 43.16 1.82
4989 5170 9.832445 TTGGAAAGAATTACTAAGCCATAGTAG 57.168 33.333 6.98 0.00 45.48 2.57
5048 5229 7.439108 AGCCTATGTCCCTATTATTACATCC 57.561 40.000 0.00 0.00 34.54 3.51
5051 5232 7.988028 GCCTATGTCCCTATTATTACATCCTTC 59.012 40.741 0.00 0.00 34.54 3.46
5066 5247 5.503927 ACATCCTTCACATTGCTATGTTCT 58.496 37.500 11.24 0.00 42.29 3.01
5078 5262 6.785488 TTGCTATGTTCTCAACTTGTACTG 57.215 37.500 0.00 0.00 0.00 2.74
5085 5269 2.813754 TCTCAACTTGTACTGCATTGCC 59.186 45.455 6.12 0.00 0.00 4.52
5096 5280 2.568090 CATTGCCTGCACGGGTTC 59.432 61.111 0.00 0.00 0.00 3.62
5123 5308 5.049129 GTCTTGTTTCCATTCTTCTGTGAGG 60.049 44.000 0.00 0.00 0.00 3.86
5176 5361 1.304282 GGCTGGGATTGGAGAAGCA 59.696 57.895 0.00 0.00 35.55 3.91
5183 5368 2.489722 GGGATTGGAGAAGCAGTTGAAC 59.510 50.000 0.00 0.00 0.00 3.18
5185 5370 1.593196 TTGGAGAAGCAGTTGAACGG 58.407 50.000 0.00 0.00 0.00 4.44
5188 5373 0.514691 GAGAAGCAGTTGAACGGCAG 59.485 55.000 21.54 0.00 41.80 4.85
5189 5374 1.081840 GAAGCAGTTGAACGGCAGC 60.082 57.895 21.54 9.58 41.80 5.25
5191 5376 1.174712 AAGCAGTTGAACGGCAGCAT 61.175 50.000 21.54 3.14 41.80 3.79
5192 5377 1.174712 AGCAGTTGAACGGCAGCATT 61.175 50.000 21.54 0.00 41.80 3.56
5193 5378 0.730494 GCAGTTGAACGGCAGCATTC 60.730 55.000 15.33 0.00 39.14 2.67
5194 5379 0.592637 CAGTTGAACGGCAGCATTCA 59.407 50.000 7.14 7.14 33.03 2.57
5197 5382 0.313672 TTGAACGGCAGCATTCAACC 59.686 50.000 16.41 0.00 39.34 3.77
5202 5387 4.481112 GCAGCATTCAACCGCCCG 62.481 66.667 0.00 0.00 0.00 6.13
5206 5391 3.202001 CATTCAACCGCCCGCGAT 61.202 61.111 8.23 0.00 42.83 4.58
5207 5392 2.437716 ATTCAACCGCCCGCGATT 60.438 55.556 8.23 0.00 42.83 3.34
5236 5421 2.360726 CCAAGGGGTTACGGCACC 60.361 66.667 0.00 0.00 35.88 5.01
5238 5423 1.001393 CAAGGGGTTACGGCACCAT 60.001 57.895 7.51 0.00 38.79 3.55
5240 5425 0.993470 AAGGGGTTACGGCACCATAA 59.007 50.000 7.51 0.00 38.79 1.90
5241 5426 1.218844 AGGGGTTACGGCACCATAAT 58.781 50.000 7.51 0.00 38.79 1.28
5242 5427 1.133915 AGGGGTTACGGCACCATAATG 60.134 52.381 7.51 0.00 38.79 1.90
5243 5428 1.314730 GGGTTACGGCACCATAATGG 58.685 55.000 7.51 0.00 45.02 3.16
5259 5444 3.452755 AATGGTGATAACGCTGATCGA 57.547 42.857 0.00 0.00 41.67 3.59
5282 5467 9.640963 TCGAAAGAAATTTTAAAACAAGTCCAA 57.359 25.926 1.97 0.00 37.03 3.53
5295 5480 7.913674 AAACAAGTCCAAATGTTTTAGCAAA 57.086 28.000 0.00 0.00 44.91 3.68
5296 5481 7.538303 AACAAGTCCAAATGTTTTAGCAAAG 57.462 32.000 0.00 0.00 36.39 2.77
5301 5486 3.674753 CCAAATGTTTTAGCAAAGCCGAG 59.325 43.478 0.00 0.00 0.00 4.63
5302 5487 3.575965 AATGTTTTAGCAAAGCCGAGG 57.424 42.857 0.00 0.00 0.00 4.63
5303 5488 1.975660 TGTTTTAGCAAAGCCGAGGT 58.024 45.000 0.00 0.00 0.00 3.85
5304 5489 2.303175 TGTTTTAGCAAAGCCGAGGTT 58.697 42.857 0.00 0.00 0.00 3.50
5315 5500 5.263185 CAAAGCCGAGGTTTAATGTTATCG 58.737 41.667 1.64 0.00 31.81 2.92
5316 5501 2.870411 AGCCGAGGTTTAATGTTATCGC 59.130 45.455 0.00 0.00 0.00 4.58
5317 5502 2.870411 GCCGAGGTTTAATGTTATCGCT 59.130 45.455 0.00 0.00 0.00 4.93
5328 5513 1.741145 TGTTATCGCTGCGTCTAGACA 59.259 47.619 22.48 16.33 0.00 3.41
5340 5525 0.956633 TCTAGACAAGAACACGCGGT 59.043 50.000 12.47 2.05 0.00 5.68
5341 5526 1.060713 CTAGACAAGAACACGCGGTG 58.939 55.000 12.47 9.20 39.75 4.94
5350 5535 4.671549 CACGCGGTGTGCTTGCAG 62.672 66.667 12.47 0.00 42.70 4.41
5352 5537 3.952675 CGCGGTGTGCTTGCAGTT 61.953 61.111 0.00 0.00 43.27 3.16
5353 5538 2.353839 GCGGTGTGCTTGCAGTTG 60.354 61.111 0.00 0.00 41.73 3.16
5354 5539 2.353839 CGGTGTGCTTGCAGTTGC 60.354 61.111 0.00 0.00 42.50 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.790043 GGTGCGCGCAATTTAGTTTTT 59.210 42.857 38.24 0.00 0.00 1.94
9 10 1.414378 GGTGCGCGCAATTTAGTTTT 58.586 45.000 38.24 0.00 0.00 2.43
10 11 0.727793 CGGTGCGCGCAATTTAGTTT 60.728 50.000 38.24 0.00 0.00 2.66
11 12 1.154301 CGGTGCGCGCAATTTAGTT 60.154 52.632 38.24 0.00 0.00 2.24
58 60 9.833894 CGTATTGATTTTCTCAACAACAAAAAG 57.166 29.630 0.00 0.00 46.37 2.27
77 80 3.042871 ACGCCAAAAGGTACGTATTGA 57.957 42.857 7.96 0.00 36.91 2.57
236 243 0.680061 GACGGAGAACTGAACTGGGT 59.320 55.000 0.00 0.00 0.00 4.51
244 251 2.610727 GGGAGAAACTGACGGAGAACTG 60.611 54.545 0.00 0.00 0.00 3.16
310 318 1.288127 GCCACCTGTAGAACGACGT 59.712 57.895 0.00 0.00 0.00 4.34
328 336 1.724581 GTCGCGAAAAACCTTGCCG 60.725 57.895 12.06 0.00 0.00 5.69
347 356 0.094730 GGACGAACCGCGAATTTCTG 59.905 55.000 8.23 6.54 44.57 3.02
392 401 1.672145 GGGTAGATTTATCCCGCGCTC 60.672 57.143 5.56 0.00 0.00 5.03
468 477 3.150767 GGTCTATGGCGTAGATGAGACT 58.849 50.000 18.82 0.00 41.33 3.24
488 497 4.679662 AGATTTCACGGTATCTGTAACGG 58.320 43.478 0.00 0.00 45.18 4.44
563 572 7.016153 TGGTCATCAGTAGTAGGAAAATTGT 57.984 36.000 0.00 0.00 0.00 2.71
574 584 4.889995 TCGATCTCAATGGTCATCAGTAGT 59.110 41.667 0.00 0.00 0.00 2.73
581 591 4.037208 GCCAAAATCGATCTCAATGGTCAT 59.963 41.667 0.00 0.00 0.00 3.06
597 607 4.626046 GCATGATACCCAAAAGGCCAAAAT 60.626 41.667 5.01 0.00 40.58 1.82
634 644 8.411683 CAGAACACCTTATATACGACCTAAACT 58.588 37.037 0.00 0.00 0.00 2.66
724 734 3.921677 TCAGCTTCCGTCGTTTATCTTT 58.078 40.909 0.00 0.00 0.00 2.52
731 741 1.289380 GACCTCAGCTTCCGTCGTT 59.711 57.895 0.00 0.00 0.00 3.85
775 785 7.859325 TTGCCCATTTAACTACAGAATAGAC 57.141 36.000 0.00 0.00 0.00 2.59
794 804 2.052782 ATGTCTACCGGATTTTGCCC 57.947 50.000 9.46 0.00 0.00 5.36
849 859 3.897239 TGACAGGAAAGAAAGCAGGAAA 58.103 40.909 0.00 0.00 0.00 3.13
1013 1052 7.095940 CCATTGTGTCTGCAGTTAAAGAAAATG 60.096 37.037 14.67 9.52 36.25 2.32
1059 1098 5.006386 CCAGGGAGATTGCCTACATAAATC 58.994 45.833 0.00 0.00 35.31 2.17
1135 1174 6.744537 GCTAGTGCAAGAATCATTACACAAAG 59.255 38.462 0.00 0.00 39.41 2.77
1187 1226 7.859377 CAGTTTGTGCTATAGCCAATTATCTTG 59.141 37.037 21.84 12.02 41.18 3.02
1261 1300 6.483640 GCTGCAACCTATAGCATACTAGTTTT 59.516 38.462 0.00 0.00 40.42 2.43
1292 1331 9.277565 CGTTTTAATTCCTTACAATGAGATGTG 57.722 33.333 0.00 0.00 34.75 3.21
1298 1337 7.527568 AACCCGTTTTAATTCCTTACAATGA 57.472 32.000 0.00 0.00 0.00 2.57
1318 1357 9.830975 ACATAAAATTAAGGCATGAATAAACCC 57.169 29.630 0.00 0.00 0.00 4.11
1457 1496 3.702045 GAGTACAAGCCTCATAGGACAGT 59.298 47.826 0.00 0.00 37.67 3.55
1474 1513 7.044798 AGGCTTCTATCACAAATTCTGAGTAC 58.955 38.462 0.00 0.00 0.00 2.73
1487 1526 8.910351 AATAGGAACAATAAGGCTTCTATCAC 57.090 34.615 1.30 0.00 0.00 3.06
1582 1622 9.183368 GGATCCTCAAACTAAAGAAGATCATTT 57.817 33.333 3.84 0.00 34.76 2.32
1639 1679 2.549754 GCCATCAAAGTCATACCCATCG 59.450 50.000 0.00 0.00 0.00 3.84
1680 1720 1.675552 AAAAGGCAACACGCAGTACT 58.324 45.000 0.00 0.00 41.61 2.73
1726 1766 2.874849 ACTTTTCAAACAACAGGCACG 58.125 42.857 0.00 0.00 0.00 5.34
1799 1839 1.089481 TAAAGCTGCTTGGGCGATCG 61.089 55.000 16.73 11.69 42.25 3.69
1896 1936 9.430399 AAATGAGAATTCCAATCCAGACATATT 57.570 29.630 0.65 0.00 0.00 1.28
1904 1944 8.426569 AGAAGAAAAATGAGAATTCCAATCCA 57.573 30.769 0.65 0.00 0.00 3.41
1909 1949 8.469309 ACAAGAGAAGAAAAATGAGAATTCCA 57.531 30.769 0.65 0.28 0.00 3.53
1928 1968 1.159713 TGTGTGGCTCGCAACAAGAG 61.160 55.000 0.00 0.00 38.68 2.85
1937 1977 1.464608 CAACCATAACTGTGTGGCTCG 59.535 52.381 11.21 0.00 39.60 5.03
2044 2084 1.393603 TCGCCAACCAAACACAATGA 58.606 45.000 0.00 0.00 0.00 2.57
2050 2090 0.950836 CAGACATCGCCAACCAAACA 59.049 50.000 0.00 0.00 0.00 2.83
2098 2138 7.225931 GTCGCATATGGTCCTGAATAAGTAAAA 59.774 37.037 4.56 0.00 0.00 1.52
2099 2139 6.704493 GTCGCATATGGTCCTGAATAAGTAAA 59.296 38.462 4.56 0.00 0.00 2.01
2211 2252 3.002791 TCCTCAAATTTCTAGTGCGCAG 58.997 45.455 12.22 0.00 0.00 5.18
2416 2457 4.986659 TCACTAAAAAGCGGAGTGTAGAAC 59.013 41.667 0.00 0.00 41.14 3.01
2417 2458 5.204409 TCACTAAAAAGCGGAGTGTAGAA 57.796 39.130 0.00 0.00 41.14 2.10
2453 2497 7.812191 ACAGCAATCGATGATAGAGAATAGTTC 59.188 37.037 0.00 0.00 31.28 3.01
2497 2541 0.317160 CATATCGCCAAGACGCCCTA 59.683 55.000 0.00 0.00 0.00 3.53
2503 2547 2.747446 ACAAACCACATATCGCCAAGAC 59.253 45.455 0.00 0.00 0.00 3.01
2504 2548 3.066291 ACAAACCACATATCGCCAAGA 57.934 42.857 0.00 0.00 0.00 3.02
2514 2558 6.337356 CAACTAAAACAGGAACAAACCACAT 58.663 36.000 0.00 0.00 0.00 3.21
2561 2605 6.112734 TCGAGCTTCCTAATCTGCAAAATTA 58.887 36.000 0.00 0.00 0.00 1.40
2660 2704 6.049149 GCAGATGCCATCTTAACTACTGTTA 58.951 40.000 3.97 0.00 37.58 2.41
2687 2731 5.856126 TGCTAGTGTAAAATCAAACGGAG 57.144 39.130 0.00 0.00 0.00 4.63
2691 2735 9.282247 CAGATTCATGCTAGTGTAAAATCAAAC 57.718 33.333 0.00 0.00 0.00 2.93
2744 2788 6.453943 TGCTTCTTGATCTAGCATCATACTC 58.546 40.000 0.00 0.00 39.79 2.59
2835 2879 7.425606 ACTTGTCATGAAACTTGGTGTAAATC 58.574 34.615 0.00 0.00 0.00 2.17
3114 3159 6.068010 AGGTAGACATCAAAACAACCATTCA 58.932 36.000 0.00 0.00 0.00 2.57
3152 3198 8.140677 TCAATTTAAACTGCCAAAACATCTTG 57.859 30.769 0.00 0.00 0.00 3.02
3188 3234 6.070767 CCCTCTCTGTTCCTAAATACAAGTCA 60.071 42.308 0.00 0.00 0.00 3.41
3194 3240 7.842887 AGATACCCTCTCTGTTCCTAAATAC 57.157 40.000 0.00 0.00 0.00 1.89
3268 3314 7.432838 CCGAGCTAACAGTAAAAAGAGATAGAC 59.567 40.741 0.00 0.00 0.00 2.59
3281 3327 2.502142 TGGAGTCCGAGCTAACAGTA 57.498 50.000 4.30 0.00 0.00 2.74
3511 3568 5.510520 CCTTACTATCAGGACCATCTTGCTC 60.511 48.000 0.00 0.00 32.41 4.26
3664 3723 8.057623 ACAACATTTCCCATTCATCTTCTCTAT 58.942 33.333 0.00 0.00 0.00 1.98
3853 3913 7.016153 AGAAAGTAACCAAGACATACATCCA 57.984 36.000 0.00 0.00 0.00 3.41
4014 4074 8.759481 AATCCAAAATTAACACCAAAACCAAT 57.241 26.923 0.00 0.00 0.00 3.16
4044 4104 5.760253 ACCAAGTTCATTACTCAGAAGTGTG 59.240 40.000 0.00 0.00 35.54 3.82
4093 4153 3.025322 ACAGGAGACCGAGATCTTGAT 57.975 47.619 11.89 0.00 0.00 2.57
4117 4177 7.011482 GCTAATTGATTGTCGAGACTTACCAAT 59.989 37.037 4.78 6.41 0.00 3.16
4119 4179 5.810587 GCTAATTGATTGTCGAGACTTACCA 59.189 40.000 4.78 0.00 0.00 3.25
4138 4198 5.163405 TGGCTCGAGTAAAGATTCTGCTAAT 60.163 40.000 15.13 0.00 0.00 1.73
4141 4201 2.497675 TGGCTCGAGTAAAGATTCTGCT 59.502 45.455 15.13 0.00 0.00 4.24
4289 4350 8.066595 CAGAAGTTAATCATAAGCGATTTCTGG 58.933 37.037 0.00 0.00 35.14 3.86
4290 4351 7.585573 GCAGAAGTTAATCATAAGCGATTTCTG 59.414 37.037 0.00 0.00 38.45 3.02
4313 4374 4.813161 CCAGAACAGACACCATATTAGCAG 59.187 45.833 0.00 0.00 0.00 4.24
4356 4417 2.361610 CTTCCAGGTGCGCCCAAT 60.362 61.111 14.07 0.00 34.66 3.16
4396 4458 3.196901 ACCACCTACGATGAATACTTGCA 59.803 43.478 0.00 0.00 0.00 4.08
4399 4461 3.490419 GCGACCACCTACGATGAATACTT 60.490 47.826 0.00 0.00 0.00 2.24
4407 4469 1.961394 ACATATGCGACCACCTACGAT 59.039 47.619 1.58 0.00 0.00 3.73
4419 4481 4.092529 GCAGGACATGATAGAACATATGCG 59.907 45.833 1.58 0.00 0.00 4.73
4427 4489 4.058124 GCGTTATGCAGGACATGATAGAA 58.942 43.478 0.00 0.00 45.45 2.10
4549 4611 3.326880 TCAAGAAAAGGTACAGGTCTCCC 59.673 47.826 0.00 0.00 0.00 4.30
4613 4675 3.325135 CCACAAAGTACAGGTCTCCTCTT 59.675 47.826 0.00 0.00 0.00 2.85
4626 4688 8.453238 ACAACATAACACATTACCACAAAGTA 57.547 30.769 0.00 0.00 0.00 2.24
4667 4729 7.490079 CGTGCTTATTACCAACATAGAGTTACA 59.510 37.037 0.00 0.00 38.74 2.41
4681 4744 2.234300 TGCTAGCCGTGCTTATTACC 57.766 50.000 13.29 0.00 40.44 2.85
4697 4760 6.528537 TGAAAAACATAATGTGGCTATGCT 57.471 33.333 0.00 0.00 31.12 3.79
4723 4786 0.106918 GTCCACAACAACCACCTGGA 60.107 55.000 0.00 0.00 38.94 3.86
4736 4799 4.758251 CAGGCATCGGCGTCCACA 62.758 66.667 6.85 0.00 42.47 4.17
4747 4810 1.106351 ACGAGCTCGAGATCAGGCAT 61.106 55.000 40.58 13.00 43.02 4.40
4748 4811 1.719725 GACGAGCTCGAGATCAGGCA 61.720 60.000 40.58 0.00 43.02 4.75
4750 4813 1.278337 CGACGAGCTCGAGATCAGG 59.722 63.158 40.58 16.44 46.14 3.86
4752 4815 2.710086 GCGACGAGCTCGAGATCA 59.290 61.111 40.58 0.00 46.14 2.92
4774 4837 2.439338 AGTGGCGTTGGTGCACAA 60.439 55.556 20.43 3.78 36.54 3.33
4785 4848 4.742201 CCTCGGACACCAGTGGCG 62.742 72.222 9.78 1.17 40.25 5.69
4846 5001 1.202582 ACCTCGATCGCCTATGTATGC 59.797 52.381 11.09 0.00 0.00 3.14
4869 5024 2.892425 CGCCACGAAGAGCCCATC 60.892 66.667 0.00 0.00 0.00 3.51
4873 5028 3.127533 AATGCGCCACGAAGAGCC 61.128 61.111 4.18 0.00 0.00 4.70
4874 5029 2.099062 CAATGCGCCACGAAGAGC 59.901 61.111 4.18 0.00 0.00 4.09
4876 5031 0.665835 AAAACAATGCGCCACGAAGA 59.334 45.000 4.18 0.00 0.00 2.87
4877 5032 1.189884 CAAAAACAATGCGCCACGAAG 59.810 47.619 4.18 0.00 0.00 3.79
4878 5033 1.202302 TCAAAAACAATGCGCCACGAA 60.202 42.857 4.18 0.00 0.00 3.85
4920 5098 8.080417 GCTGAAATACGAGTATATTGGTCTGTA 58.920 37.037 0.00 0.00 0.00 2.74
4927 5105 8.855279 GCTCTTAGCTGAAATACGAGTATATTG 58.145 37.037 0.00 0.00 38.45 1.90
4928 5106 8.577296 TGCTCTTAGCTGAAATACGAGTATATT 58.423 33.333 0.00 0.00 42.97 1.28
4933 5111 4.082190 TGTGCTCTTAGCTGAAATACGAGT 60.082 41.667 0.00 0.00 42.97 4.18
4978 5159 4.137543 GCTTTGTATGGCTACTATGGCTT 58.862 43.478 0.00 0.00 0.00 4.35
4987 5168 4.381825 CCATTTGCTTGCTTTGTATGGCTA 60.382 41.667 0.00 0.00 0.00 3.93
4988 5169 3.592059 CATTTGCTTGCTTTGTATGGCT 58.408 40.909 0.00 0.00 0.00 4.75
4989 5170 2.674357 CCATTTGCTTGCTTTGTATGGC 59.326 45.455 0.00 0.00 0.00 4.40
5048 5229 6.492007 AGTTGAGAACATAGCAATGTGAAG 57.508 37.500 0.00 0.00 45.79 3.02
5051 5232 6.005583 ACAAGTTGAGAACATAGCAATGTG 57.994 37.500 10.54 0.00 45.79 3.21
5066 5247 2.553602 CAGGCAATGCAGTACAAGTTGA 59.446 45.455 10.54 0.00 0.00 3.18
5085 5269 0.588252 CAAGACAAGAACCCGTGCAG 59.412 55.000 0.00 0.00 0.00 4.41
5143 5328 0.738389 CAGCCCGCGTGGAAATAAAT 59.262 50.000 18.79 0.00 37.49 1.40
5171 5356 1.081840 GCTGCCGTTCAACTGCTTC 60.082 57.895 5.47 0.00 0.00 3.86
5176 5361 1.317613 TTGAATGCTGCCGTTCAACT 58.682 45.000 19.71 0.00 46.58 3.16
5183 5368 4.481112 GGCGGTTGAATGCTGCCG 62.481 66.667 0.00 2.66 46.81 5.69
5185 5370 4.481112 CGGGCGGTTGAATGCTGC 62.481 66.667 0.00 0.00 37.50 5.25
5189 5374 2.760159 AATCGCGGGCGGTTGAATG 61.760 57.895 11.17 0.00 41.57 2.67
5202 5387 4.120331 GTGGGCTGGTGCAATCGC 62.120 66.667 0.00 0.00 41.91 4.58
5206 5391 2.521465 CTTGGTGGGCTGGTGCAA 60.521 61.111 0.00 0.00 41.91 4.08
5207 5392 4.601794 CCTTGGTGGGCTGGTGCA 62.602 66.667 0.00 0.00 41.91 4.57
5234 5419 6.306015 CGATCAGCGTTATCACCATTATGGT 61.306 44.000 11.67 11.67 43.28 3.55
5235 5420 4.091945 CGATCAGCGTTATCACCATTATGG 59.908 45.833 10.08 10.08 38.28 2.74
5236 5421 4.923281 TCGATCAGCGTTATCACCATTATG 59.077 41.667 0.00 0.00 41.80 1.90
5238 5423 4.577834 TCGATCAGCGTTATCACCATTA 57.422 40.909 0.00 0.00 41.80 1.90
5240 5425 3.452755 TTCGATCAGCGTTATCACCAT 57.547 42.857 0.00 0.00 41.80 3.55
5241 5426 2.951457 TTCGATCAGCGTTATCACCA 57.049 45.000 0.00 0.00 41.80 4.17
5242 5427 3.444916 TCTTTCGATCAGCGTTATCACC 58.555 45.455 0.00 0.00 41.80 4.02
5243 5428 5.450376 TTTCTTTCGATCAGCGTTATCAC 57.550 39.130 0.00 0.00 41.80 3.06
5244 5429 6.662414 AATTTCTTTCGATCAGCGTTATCA 57.338 33.333 0.00 0.00 41.80 2.15
5245 5430 7.954906 AAAATTTCTTTCGATCAGCGTTATC 57.045 32.000 0.00 0.00 41.80 1.75
5277 5462 3.428534 CGGCTTTGCTAAAACATTTGGAC 59.571 43.478 0.00 0.00 0.00 4.02
5279 5464 3.648009 TCGGCTTTGCTAAAACATTTGG 58.352 40.909 0.00 0.00 0.00 3.28
5282 5467 2.890945 ACCTCGGCTTTGCTAAAACATT 59.109 40.909 0.00 0.00 0.00 2.71
5295 5480 2.870411 GCGATAACATTAAACCTCGGCT 59.130 45.455 0.00 0.00 0.00 5.52
5296 5481 2.870411 AGCGATAACATTAAACCTCGGC 59.130 45.455 0.00 0.00 0.00 5.54
5301 5486 3.308866 AGACGCAGCGATAACATTAAACC 59.691 43.478 24.65 0.00 0.00 3.27
5302 5487 4.516092 AGACGCAGCGATAACATTAAAC 57.484 40.909 24.65 0.00 0.00 2.01
5303 5488 5.457799 GTCTAGACGCAGCGATAACATTAAA 59.542 40.000 24.65 0.00 0.00 1.52
5304 5489 4.974275 GTCTAGACGCAGCGATAACATTAA 59.026 41.667 24.65 0.00 0.00 1.40
5315 5500 1.721926 GTGTTCTTGTCTAGACGCAGC 59.278 52.381 17.85 6.87 30.90 5.25
5316 5501 1.979469 CGTGTTCTTGTCTAGACGCAG 59.021 52.381 17.85 15.41 30.90 5.18
5317 5502 1.929038 GCGTGTTCTTGTCTAGACGCA 60.929 52.381 17.85 6.41 43.31 5.24
5328 5513 1.817941 AAGCACACCGCGTGTTCTT 60.818 52.632 16.20 16.20 45.08 2.52


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

AutoCloner maintained by Alex Coulton.