Multiple sequence alignment - TraesCS7B01G175500

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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 TraesCS7B01G175500 chr7B 100.000 4212 0 0 1 4212 247242908 247247119 0.000000e+00 7779.0
1 TraesCS7B01G175500 chr7D 95.305 2492 51 19 1 2469 266899490 266897042 0.000000e+00 3893.0
2 TraesCS7B01G175500 chr7D 96.226 1484 35 11 2417 3894 266897042 266895574 0.000000e+00 2410.0
3 TraesCS7B01G175500 chr7D 89.412 170 13 2 4042 4211 88146075 88146239 4.270000e-50 209.0
4 TraesCS7B01G175500 chr7D 87.931 174 18 3 4040 4212 99194918 99194747 7.140000e-48 202.0
5 TraesCS7B01G175500 chr7A 97.380 2061 31 12 1406 3451 292850152 292848100 0.000000e+00 3485.0
6 TraesCS7B01G175500 chr7A 95.442 1426 34 14 1 1409 292851655 292850244 0.000000e+00 2244.0
7 TraesCS7B01G175500 chr7A 92.845 587 35 5 3446 4029 292848053 292847471 0.000000e+00 845.0
8 TraesCS7B01G175500 chr7A 92.025 163 9 3 3872 4032 292847473 292847313 4.240000e-55 226.0
9 TraesCS7B01G175500 chr7A 97.222 36 1 0 3486 3521 292848087 292848052 1.260000e-05 62.1
10 TraesCS7B01G175500 chr2D 91.860 172 14 0 4041 4212 142030207 142030036 1.510000e-59 241.0
11 TraesCS7B01G175500 chr2D 88.304 171 20 0 4042 4212 638393276 638393106 5.520000e-49 206.0
12 TraesCS7B01G175500 chr6D 92.216 167 13 0 4046 4212 414103346 414103512 1.960000e-58 237.0
13 TraesCS7B01G175500 chr4A 91.228 171 15 0 4042 4212 563086119 563085949 2.530000e-57 233.0
14 TraesCS7B01G175500 chr4A 83.951 162 23 3 3872 4031 163767098 163766938 7.290000e-33 152.0
15 TraesCS7B01G175500 chr4A 76.101 159 36 2 3876 4032 12650373 12650531 9.710000e-12 82.4
16 TraesCS7B01G175500 chr1B 89.941 169 17 0 4044 4212 84974802 84974634 7.090000e-53 219.0
17 TraesCS7B01G175500 chr5A 88.690 168 18 1 4044 4211 488040724 488040890 1.990000e-48 204.0
18 TraesCS7B01G175500 chr3B 87.791 172 21 0 4040 4211 737335544 737335715 7.140000e-48 202.0
19 TraesCS7B01G175500 chr6A 81.347 193 29 6 3842 4032 53082695 53082882 2.620000e-32 150.0
20 TraesCS7B01G175500 chr5D 82.911 158 25 1 3877 4032 400405309 400405152 1.580000e-29 141.0
21 TraesCS7B01G175500 chr4D 85.000 140 19 2 3877 4014 312917899 312918038 1.580000e-29 141.0
22 TraesCS7B01G175500 chr4D 86.066 122 17 0 3893 4014 312937993 312938114 9.500000e-27 132.0
23 TraesCS7B01G175500 chr4D 84.000 125 17 2 3890 4014 21772491 21772370 2.660000e-22 117.0
24 TraesCS7B01G175500 chr1D 87.143 70 3 3 3779 3848 468820 468883 1.620000e-09 75.0
25 TraesCS7B01G175500 chr1A 93.750 48 3 0 3779 3826 3466083 3466036 5.840000e-09 73.1


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 TraesCS7B01G175500 chr7B 247242908 247247119 4211 False 7779.00 7779 100.0000 1 4212 1 chr7B.!!$F1 4211
1 TraesCS7B01G175500 chr7D 266895574 266899490 3916 True 3151.50 3893 95.7655 1 3894 2 chr7D.!!$R2 3893
2 TraesCS7B01G175500 chr7A 292847313 292851655 4342 True 1372.42 3485 94.9828 1 4032 5 chr7A.!!$R1 4031

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
167 191 0.323816 TCCTCACTCTCATGCGTCCT 60.324 55.000 0.00 0.0 0.00 3.85 F
439 464 0.439214 CGAGCGCGTAGATAGATCGT 59.561 55.000 8.43 0.0 38.72 3.73 F
1223 1249 1.630369 TCCTTGGCATGCTTAGTCTGT 59.370 47.619 18.92 0.0 0.00 3.41 F
2393 2526 1.605710 GCTAAGGCACATGGTATGCAG 59.394 52.381 8.81 0.0 45.27 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1453 1575 0.619832 AAGCAGAGATGAGCCCTGGA 60.620 55.00 0.00 0.0 0.00 3.86 R
1893 2016 5.847111 ATGAAATCAATGACATGGAGTGG 57.153 39.13 0.00 0.0 0.00 4.00 R
2447 2632 1.484038 AGTCTTCTCAGGCTAGCCAG 58.516 55.00 34.70 27.4 31.00 4.85 R
4155 4557 0.109039 GGCCGCGGCAAATTCTTTTA 60.109 50.00 46.88 0.0 44.11 1.52 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
115 138 2.128729 GAGATCCTCGGGACAAGGG 58.871 63.158 0.00 0.00 32.98 3.95
167 191 0.323816 TCCTCACTCTCATGCGTCCT 60.324 55.000 0.00 0.00 0.00 3.85
295 319 2.416296 CCAATCGGTAACTGTGCTACGA 60.416 50.000 0.00 0.00 34.70 3.43
329 353 2.445492 TACCCGTCCCTCCCGTTTCT 62.445 60.000 0.00 0.00 0.00 2.52
348 373 6.183360 CGTTTCTGCAATATATTACCCGATCC 60.183 42.308 0.00 0.00 0.00 3.36
439 464 0.439214 CGAGCGCGTAGATAGATCGT 59.561 55.000 8.43 0.00 38.72 3.73
523 548 1.798079 GCGCGTCTCGGTTTAGATCTT 60.798 52.381 8.43 0.00 38.94 2.40
625 650 3.118149 AGGGTCGTTACAGTCCTGTTTTT 60.118 43.478 5.10 0.00 41.83 1.94
946 971 5.982516 TGTTTGTTGCTTTTGTGATATCACC 59.017 36.000 28.64 15.65 45.88 4.02
1216 1242 4.677673 GGAATAAATCCTTGGCATGCTT 57.322 40.909 18.92 4.41 45.56 3.91
1217 1243 5.789643 GGAATAAATCCTTGGCATGCTTA 57.210 39.130 18.92 6.71 45.56 3.09
1218 1244 5.776744 GGAATAAATCCTTGGCATGCTTAG 58.223 41.667 18.92 14.35 45.56 2.18
1219 1245 5.302823 GGAATAAATCCTTGGCATGCTTAGT 59.697 40.000 18.92 5.46 45.56 2.24
1220 1246 6.396829 AATAAATCCTTGGCATGCTTAGTC 57.603 37.500 18.92 0.10 0.00 2.59
1221 1247 3.659183 AATCCTTGGCATGCTTAGTCT 57.341 42.857 18.92 2.08 0.00 3.24
1222 1248 2.408271 TCCTTGGCATGCTTAGTCTG 57.592 50.000 18.92 3.29 0.00 3.51
1223 1249 1.630369 TCCTTGGCATGCTTAGTCTGT 59.370 47.619 18.92 0.00 0.00 3.41
1224 1250 2.040278 TCCTTGGCATGCTTAGTCTGTT 59.960 45.455 18.92 0.00 0.00 3.16
1225 1251 2.821969 CCTTGGCATGCTTAGTCTGTTT 59.178 45.455 18.92 0.00 0.00 2.83
1237 1263 8.534333 TGCTTAGTCTGTTTTAGTCTGTATTG 57.466 34.615 0.00 0.00 0.00 1.90
1336 1362 5.048573 GGCAGGATTACCTTTTCGTGTAAAA 60.049 40.000 0.00 0.00 45.36 1.52
1731 1853 7.713073 TGTGTTTAGTGTGTCACATTGAGATTA 59.287 33.333 9.31 0.00 36.74 1.75
2366 2499 5.843673 TTCTCTCTCAGTACCTGCATTAG 57.156 43.478 0.00 0.00 0.00 1.73
2393 2526 1.605710 GCTAAGGCACATGGTATGCAG 59.394 52.381 8.81 0.00 45.27 4.41
2422 2555 5.076182 TGGATACATTTCACACCAACACAT 58.924 37.500 0.00 0.00 46.17 3.21
2629 2816 8.985805 CCTGTAATTTTTCGTACTGTTTACTCT 58.014 33.333 0.00 0.00 0.00 3.24
2870 3057 5.689961 GCATGTCGTTTAAACCTTTGTTGAT 59.310 36.000 12.66 0.00 34.13 2.57
3016 3203 6.239402 GGAAACTGGTAACTACCTGACACTTA 60.239 42.308 16.99 0.00 46.58 2.24
3078 3265 4.848562 TCTGATGTGCCTAATACCTACG 57.151 45.455 0.00 0.00 0.00 3.51
3199 3388 2.270205 CGCAAGCTGGTCCTGGAT 59.730 61.111 0.00 0.00 0.00 3.41
3603 3844 3.375699 AGTGATAATCTGAGGGGACGTT 58.624 45.455 0.00 0.00 0.00 3.99
3604 3845 3.133003 AGTGATAATCTGAGGGGACGTTG 59.867 47.826 0.00 0.00 0.00 4.10
3624 3865 5.049060 CGTTGATTTTTGGGACATGAGTGTA 60.049 40.000 0.00 0.00 39.09 2.90
3693 3938 5.665459 AGAGCATGTACAGAGATTGGTAAC 58.335 41.667 0.33 0.00 0.00 2.50
3860 4105 1.203100 AGGCCAAGAGGATGCAAAACT 60.203 47.619 5.01 0.00 36.89 2.66
3865 4111 3.820467 CCAAGAGGATGCAAAACTGTGTA 59.180 43.478 0.00 0.00 36.89 2.90
3866 4112 4.460382 CCAAGAGGATGCAAAACTGTGTAT 59.540 41.667 0.00 0.00 36.89 2.29
3929 4177 1.537562 GGGATGTACGAGGCGGTTAAG 60.538 57.143 0.00 0.00 0.00 1.85
3963 4211 3.781770 GATCGTGCGGGAGAGGCAG 62.782 68.421 0.00 0.00 41.83 4.85
3990 4238 7.272244 TCTTGAATTATTACTCCTCATGCGAA 58.728 34.615 0.00 0.00 0.00 4.70
3994 4242 6.712241 ATTATTACTCCTCATGCGAAATCG 57.288 37.500 0.00 0.00 43.27 3.34
4005 4407 6.400834 CCTCATGCGAAATCGAGAATTATCTG 60.401 42.308 7.06 0.00 43.02 2.90
4013 4415 7.440523 AAATCGAGAATTATCTGTAATGGGC 57.559 36.000 0.00 0.00 35.54 5.36
4020 4422 6.264067 AGAATTATCTGTAATGGGCTTTCAGC 59.736 38.462 0.00 0.00 35.87 4.26
4032 4434 2.610976 GGCTTTCAGCATGCATGTGAAA 60.611 45.455 32.02 32.02 44.75 2.69
4033 4435 3.259064 GCTTTCAGCATGCATGTGAAAT 58.741 40.909 33.09 16.14 41.89 2.17
4034 4436 3.682858 GCTTTCAGCATGCATGTGAAATT 59.317 39.130 33.09 14.57 41.89 1.82
4035 4437 4.153475 GCTTTCAGCATGCATGTGAAATTT 59.847 37.500 33.09 13.31 41.89 1.82
4036 4438 5.599359 TTTCAGCATGCATGTGAAATTTG 57.401 34.783 31.42 19.28 35.24 2.32
4037 4439 3.591023 TCAGCATGCATGTGAAATTTGG 58.409 40.909 26.79 7.27 34.76 3.28
4038 4440 3.007074 TCAGCATGCATGTGAAATTTGGT 59.993 39.130 26.79 2.65 34.76 3.67
4039 4441 4.220163 TCAGCATGCATGTGAAATTTGGTA 59.780 37.500 26.79 3.65 34.76 3.25
4040 4442 5.105269 TCAGCATGCATGTGAAATTTGGTAT 60.105 36.000 26.79 0.00 34.76 2.73
4041 4443 5.583061 CAGCATGCATGTGAAATTTGGTATT 59.417 36.000 26.79 0.00 0.00 1.89
4042 4444 6.092944 CAGCATGCATGTGAAATTTGGTATTT 59.907 34.615 26.79 0.00 0.00 1.40
4043 4445 7.278203 CAGCATGCATGTGAAATTTGGTATTTA 59.722 33.333 26.79 0.00 0.00 1.40
4044 4446 7.493320 AGCATGCATGTGAAATTTGGTATTTAG 59.507 33.333 26.79 0.00 0.00 1.85
4045 4447 7.492020 GCATGCATGTGAAATTTGGTATTTAGA 59.508 33.333 26.79 0.00 0.00 2.10
4046 4448 9.027129 CATGCATGTGAAATTTGGTATTTAGAG 57.973 33.333 18.91 0.00 0.00 2.43
4047 4449 7.035004 TGCATGTGAAATTTGGTATTTAGAGC 58.965 34.615 0.00 0.00 0.00 4.09
4048 4450 7.035004 GCATGTGAAATTTGGTATTTAGAGCA 58.965 34.615 0.00 0.00 0.00 4.26
4049 4451 7.545265 GCATGTGAAATTTGGTATTTAGAGCAA 59.455 33.333 0.00 0.00 35.11 3.91
4050 4452 8.863049 CATGTGAAATTTGGTATTTAGAGCAAC 58.137 33.333 0.00 0.00 36.59 4.17
4051 4453 8.177119 TGTGAAATTTGGTATTTAGAGCAACT 57.823 30.769 0.00 0.00 36.59 3.16
4052 4454 8.296713 TGTGAAATTTGGTATTTAGAGCAACTC 58.703 33.333 0.00 0.00 36.59 3.01
4053 4455 8.515414 GTGAAATTTGGTATTTAGAGCAACTCT 58.485 33.333 0.00 2.23 43.83 3.24
4054 4456 9.733556 TGAAATTTGGTATTTAGAGCAACTCTA 57.266 29.630 0.00 0.16 41.50 2.43
4056 4458 9.959721 AAATTTGGTATTTAGAGCAACTCTAGA 57.040 29.630 4.64 1.40 42.92 2.43
4057 4459 9.959721 AATTTGGTATTTAGAGCAACTCTAGAA 57.040 29.630 4.64 3.94 42.92 2.10
4058 4460 9.606631 ATTTGGTATTTAGAGCAACTCTAGAAG 57.393 33.333 4.64 0.00 42.92 2.85
4059 4461 7.956328 TGGTATTTAGAGCAACTCTAGAAGA 57.044 36.000 4.64 0.00 42.92 2.87
4060 4462 7.773149 TGGTATTTAGAGCAACTCTAGAAGAC 58.227 38.462 4.64 8.97 42.92 3.01
4061 4463 7.147880 TGGTATTTAGAGCAACTCTAGAAGACC 60.148 40.741 21.14 21.14 42.92 3.85
4062 4464 7.068962 GGTATTTAGAGCAACTCTAGAAGACCT 59.931 40.741 20.93 4.55 42.92 3.85
4063 4465 6.518208 TTTAGAGCAACTCTAGAAGACCTC 57.482 41.667 4.64 0.00 42.92 3.85
4064 4466 3.013921 AGAGCAACTCTAGAAGACCTCG 58.986 50.000 0.00 0.00 39.28 4.63
4065 4467 1.474879 AGCAACTCTAGAAGACCTCGC 59.525 52.381 0.00 0.00 0.00 5.03
4066 4468 1.202582 GCAACTCTAGAAGACCTCGCA 59.797 52.381 0.00 0.00 0.00 5.10
4067 4469 2.352814 GCAACTCTAGAAGACCTCGCAA 60.353 50.000 0.00 0.00 0.00 4.85
4068 4470 3.861131 GCAACTCTAGAAGACCTCGCAAA 60.861 47.826 0.00 0.00 0.00 3.68
4069 4471 4.307432 CAACTCTAGAAGACCTCGCAAAA 58.693 43.478 0.00 0.00 0.00 2.44
4070 4472 4.181309 ACTCTAGAAGACCTCGCAAAAG 57.819 45.455 0.00 0.00 0.00 2.27
4071 4473 3.827302 ACTCTAGAAGACCTCGCAAAAGA 59.173 43.478 0.00 0.00 0.00 2.52
4072 4474 4.170256 CTCTAGAAGACCTCGCAAAAGAC 58.830 47.826 0.00 0.00 0.00 3.01
4073 4475 1.784525 AGAAGACCTCGCAAAAGACG 58.215 50.000 0.00 0.00 0.00 4.18
4074 4476 0.164002 GAAGACCTCGCAAAAGACGC 59.836 55.000 0.00 0.00 0.00 5.19
4081 4483 3.809990 GCAAAAGACGCGAAACCG 58.190 55.556 15.93 0.00 0.00 4.44
4100 4502 2.105323 GCAAAATTCCGGCGAGTATG 57.895 50.000 9.30 0.41 0.00 2.39
4101 4503 1.859998 GCAAAATTCCGGCGAGTATGC 60.860 52.381 9.30 7.54 0.00 3.14
4102 4504 0.655733 AAAATTCCGGCGAGTATGCG 59.344 50.000 9.30 0.00 35.06 4.73
4103 4505 1.157870 AAATTCCGGCGAGTATGCGG 61.158 55.000 9.30 0.00 35.06 5.69
4111 4513 2.027751 GAGTATGCGGGCTCGGTC 59.972 66.667 8.71 0.00 36.79 4.79
4112 4514 3.501458 GAGTATGCGGGCTCGGTCC 62.501 68.421 8.71 0.00 36.79 4.46
4113 4515 3.845259 GTATGCGGGCTCGGTCCA 61.845 66.667 8.71 0.00 36.79 4.02
4114 4516 3.078196 TATGCGGGCTCGGTCCAA 61.078 61.111 8.71 0.00 36.79 3.53
4115 4517 2.439960 TATGCGGGCTCGGTCCAAT 61.440 57.895 8.71 0.00 36.79 3.16
4116 4518 1.978455 TATGCGGGCTCGGTCCAATT 61.978 55.000 8.71 0.00 36.79 2.32
4117 4519 2.750237 GCGGGCTCGGTCCAATTT 60.750 61.111 8.71 0.00 36.79 1.82
4118 4520 2.340328 GCGGGCTCGGTCCAATTTT 61.340 57.895 8.71 0.00 36.79 1.82
4119 4521 1.800681 CGGGCTCGGTCCAATTTTC 59.199 57.895 0.00 0.00 0.00 2.29
4120 4522 1.654023 CGGGCTCGGTCCAATTTTCC 61.654 60.000 0.00 0.00 0.00 3.13
4121 4523 1.654023 GGGCTCGGTCCAATTTTCCG 61.654 60.000 6.43 6.43 44.76 4.30
4122 4524 1.654023 GGCTCGGTCCAATTTTCCGG 61.654 60.000 0.00 0.00 43.75 5.14
4123 4525 1.800681 CTCGGTCCAATTTTCCGGC 59.199 57.895 0.00 0.00 43.75 6.13
4124 4526 1.654023 CTCGGTCCAATTTTCCGGCC 61.654 60.000 0.00 0.00 43.75 6.13
4125 4527 1.974343 CGGTCCAATTTTCCGGCCA 60.974 57.895 2.24 0.00 40.49 5.36
4126 4528 1.890174 GGTCCAATTTTCCGGCCAG 59.110 57.895 2.24 0.00 0.00 4.85
4127 4529 0.610785 GGTCCAATTTTCCGGCCAGA 60.611 55.000 2.24 0.00 0.00 3.86
4128 4530 1.253100 GTCCAATTTTCCGGCCAGAA 58.747 50.000 2.24 0.00 0.00 3.02
4129 4531 1.067846 GTCCAATTTTCCGGCCAGAAC 60.068 52.381 0.00 0.00 0.00 3.01
4130 4532 0.965439 CCAATTTTCCGGCCAGAACA 59.035 50.000 0.00 0.00 0.00 3.18
4131 4533 1.342819 CCAATTTTCCGGCCAGAACAA 59.657 47.619 0.00 0.19 0.00 2.83
4132 4534 2.224161 CCAATTTTCCGGCCAGAACAAA 60.224 45.455 0.00 0.00 0.00 2.83
4133 4535 3.059166 CAATTTTCCGGCCAGAACAAAG 58.941 45.455 0.00 0.00 0.00 2.77
4134 4536 0.387565 TTTTCCGGCCAGAACAAAGC 59.612 50.000 0.00 0.00 0.00 3.51
4135 4537 1.460273 TTTCCGGCCAGAACAAAGCC 61.460 55.000 0.00 0.00 43.53 4.35
4138 4540 2.653115 GGCCAGAACAAAGCCAGC 59.347 61.111 0.00 0.00 46.34 4.85
4139 4541 2.202395 GGCCAGAACAAAGCCAGCA 61.202 57.895 0.00 0.00 46.34 4.41
4140 4542 1.538687 GGCCAGAACAAAGCCAGCAT 61.539 55.000 0.00 0.00 46.34 3.79
4141 4543 1.176527 GCCAGAACAAAGCCAGCATA 58.823 50.000 0.00 0.00 0.00 3.14
4142 4544 1.135286 GCCAGAACAAAGCCAGCATAC 60.135 52.381 0.00 0.00 0.00 2.39
4143 4545 2.440409 CCAGAACAAAGCCAGCATACT 58.560 47.619 0.00 0.00 0.00 2.12
4144 4546 2.421424 CCAGAACAAAGCCAGCATACTC 59.579 50.000 0.00 0.00 0.00 2.59
4145 4547 2.094894 CAGAACAAAGCCAGCATACTCG 59.905 50.000 0.00 0.00 0.00 4.18
4146 4548 0.804989 AACAAAGCCAGCATACTCGC 59.195 50.000 0.00 0.00 0.00 5.03
4147 4549 1.026718 ACAAAGCCAGCATACTCGCC 61.027 55.000 0.00 0.00 28.88 5.54
4148 4550 1.452108 AAAGCCAGCATACTCGCCC 60.452 57.895 0.00 0.00 28.88 6.13
4149 4551 2.893682 AAAGCCAGCATACTCGCCCC 62.894 60.000 0.00 0.00 28.88 5.80
4156 4558 4.900704 ATACTCGCCCCGCCCGTA 62.901 66.667 0.00 0.00 0.00 4.02
4159 4561 4.763646 CTCGCCCCGCCCGTAAAA 62.764 66.667 0.00 0.00 0.00 1.52
4160 4562 4.763646 TCGCCCCGCCCGTAAAAG 62.764 66.667 0.00 0.00 0.00 2.27
4161 4563 4.763646 CGCCCCGCCCGTAAAAGA 62.764 66.667 0.00 0.00 0.00 2.52
4162 4564 2.360225 GCCCCGCCCGTAAAAGAA 60.360 61.111 0.00 0.00 0.00 2.52
4163 4565 1.751544 GCCCCGCCCGTAAAAGAAT 60.752 57.895 0.00 0.00 0.00 2.40
4164 4566 1.317431 GCCCCGCCCGTAAAAGAATT 61.317 55.000 0.00 0.00 0.00 2.17
4165 4567 1.179152 CCCCGCCCGTAAAAGAATTT 58.821 50.000 0.00 0.00 42.41 1.82
4166 4568 1.135228 CCCCGCCCGTAAAAGAATTTG 60.135 52.381 0.00 0.00 39.02 2.32
4167 4569 1.624487 CCGCCCGTAAAAGAATTTGC 58.376 50.000 0.00 0.00 39.02 3.68
4168 4570 1.624487 CGCCCGTAAAAGAATTTGCC 58.376 50.000 0.00 0.00 39.02 4.52
4169 4571 1.624487 GCCCGTAAAAGAATTTGCCG 58.376 50.000 0.00 0.00 39.02 5.69
4170 4572 1.624487 CCCGTAAAAGAATTTGCCGC 58.376 50.000 0.00 0.00 39.02 6.53
4171 4573 1.255767 CCGTAAAAGAATTTGCCGCG 58.744 50.000 0.00 0.00 39.02 6.46
4172 4574 1.255767 CGTAAAAGAATTTGCCGCGG 58.744 50.000 24.05 24.05 39.02 6.46
4173 4575 0.989164 GTAAAAGAATTTGCCGCGGC 59.011 50.000 42.35 42.35 39.02 6.53
4174 4576 0.109039 TAAAAGAATTTGCCGCGGCC 60.109 50.000 44.42 29.47 39.02 6.13
4175 4577 1.815817 AAAAGAATTTGCCGCGGCCT 61.816 50.000 44.42 31.22 39.02 5.19
4176 4578 2.490993 AAAGAATTTGCCGCGGCCTG 62.491 55.000 44.42 12.21 36.60 4.85
4193 4595 3.372730 GCAAACTGCATGCCCCGA 61.373 61.111 16.68 0.00 44.26 5.14
4194 4596 2.568090 CAAACTGCATGCCCCGAC 59.432 61.111 16.68 0.00 0.00 4.79
4195 4597 2.676471 AAACTGCATGCCCCGACC 60.676 61.111 16.68 0.00 0.00 4.79
4196 4598 3.505790 AAACTGCATGCCCCGACCA 62.506 57.895 16.68 0.00 0.00 4.02
4197 4599 4.722700 ACTGCATGCCCCGACCAC 62.723 66.667 16.68 0.00 0.00 4.16
4198 4600 4.415150 CTGCATGCCCCGACCACT 62.415 66.667 16.68 0.00 0.00 4.00
4199 4601 3.006133 TGCATGCCCCGACCACTA 61.006 61.111 16.68 0.00 0.00 2.74
4200 4602 2.329539 CTGCATGCCCCGACCACTAT 62.330 60.000 16.68 0.00 0.00 2.12
4201 4603 1.051556 TGCATGCCCCGACCACTATA 61.052 55.000 16.68 0.00 0.00 1.31
4202 4604 0.324943 GCATGCCCCGACCACTATAT 59.675 55.000 6.36 0.00 0.00 0.86
4203 4605 1.676014 GCATGCCCCGACCACTATATC 60.676 57.143 6.36 0.00 0.00 1.63
4204 4606 1.902508 CATGCCCCGACCACTATATCT 59.097 52.381 0.00 0.00 0.00 1.98
4205 4607 2.984435 TGCCCCGACCACTATATCTA 57.016 50.000 0.00 0.00 0.00 1.98
4206 4608 2.522185 TGCCCCGACCACTATATCTAC 58.478 52.381 0.00 0.00 0.00 2.59
4207 4609 1.471684 GCCCCGACCACTATATCTACG 59.528 57.143 0.00 0.00 0.00 3.51
4208 4610 2.089980 CCCCGACCACTATATCTACGG 58.910 57.143 0.00 0.00 38.83 4.02
4209 4611 2.553904 CCCCGACCACTATATCTACGGT 60.554 54.545 0.00 0.00 37.67 4.83
4210 4612 3.152341 CCCGACCACTATATCTACGGTT 58.848 50.000 0.00 0.00 37.67 4.44
4211 4613 3.190118 CCCGACCACTATATCTACGGTTC 59.810 52.174 0.00 0.00 37.67 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.873883 GTCGCGGATCGGTCTCGT 61.874 66.667 6.13 0.00 39.05 4.18
167 191 0.537143 AGGCTTTGTGGCGATGTGAA 60.537 50.000 0.00 0.00 46.88 3.18
295 319 1.002087 CGGGTAGAAAGCAGTGAAGGT 59.998 52.381 0.00 0.00 0.00 3.50
329 353 4.131649 CCGGATCGGGTAATATATTGCA 57.868 45.455 14.46 0.00 44.15 4.08
348 373 2.105128 GACCGGAGCAGATCACCG 59.895 66.667 9.46 11.67 46.50 4.94
439 464 1.003839 ATTCGCAGAGGAAACGGCA 60.004 52.632 0.00 0.00 38.43 5.69
523 548 0.548197 AGTAACACCAATCCCCCGGA 60.548 55.000 0.73 0.00 35.55 5.14
625 650 3.980646 CACACGAAATGAAGGTGGAAA 57.019 42.857 0.00 0.00 36.02 3.13
630 655 3.007940 TGATCTCCACACGAAATGAAGGT 59.992 43.478 0.00 0.00 0.00 3.50
781 806 5.419788 TCAGAAGGATATGTTGCAAAATGCT 59.580 36.000 12.62 8.84 45.31 3.79
782 807 5.653507 TCAGAAGGATATGTTGCAAAATGC 58.346 37.500 12.62 6.72 45.29 3.56
946 971 6.485313 TGTGTTATAGAAACAAGTTGGACTGG 59.515 38.462 7.96 0.00 31.20 4.00
1007 1033 2.274104 GGTTAATGCCCCTGCCGA 59.726 61.111 0.00 0.00 36.33 5.54
1057 1083 4.061596 AGTTCTGAGAAAGCACTTACAGC 58.938 43.478 0.00 0.00 26.34 4.40
1217 1243 9.614792 AAAACTCAATACAGACTAAAACAGACT 57.385 29.630 0.00 0.00 0.00 3.24
1336 1362 6.169094 CGGCATTGAGAACTATCCATTCTAT 58.831 40.000 0.00 0.00 36.53 1.98
1453 1575 0.619832 AAGCAGAGATGAGCCCTGGA 60.620 55.000 0.00 0.00 0.00 3.86
1893 2016 5.847111 ATGAAATCAATGACATGGAGTGG 57.153 39.130 0.00 0.00 0.00 4.00
2393 2526 7.066887 TGTTGGTGTGAAATGTATCCATATGAC 59.933 37.037 3.65 0.00 0.00 3.06
2422 2555 9.699410 AGAAATCCTAATTGTGGAATGTATTCA 57.301 29.630 6.90 0.00 38.53 2.57
2447 2632 1.484038 AGTCTTCTCAGGCTAGCCAG 58.516 55.000 34.70 27.40 31.00 4.85
2674 2861 7.829211 ACTAATGCCAAAAGAGTCTATTAGCAA 59.171 33.333 14.16 0.99 32.61 3.91
2870 3057 5.708230 AGACAACAATTTACGCATTAAGGGA 59.292 36.000 0.00 0.00 0.00 4.20
3016 3203 5.818857 ACGGTGTGTAACTTTTACATGAGTT 59.181 36.000 0.00 0.72 39.32 3.01
3492 3733 3.209410 GGATGGGCAAGACAATAGACAG 58.791 50.000 0.00 0.00 0.00 3.51
3603 3844 4.764823 GGTACACTCATGTCCCAAAAATCA 59.235 41.667 0.00 0.00 40.48 2.57
3604 3845 4.764823 TGGTACACTCATGTCCCAAAAATC 59.235 41.667 0.00 0.00 41.57 2.17
3624 3865 5.866335 TTACGAATTTAAAGCGTCATGGT 57.134 34.783 18.40 2.84 39.24 3.55
3627 3868 6.193959 GCGAATTTACGAATTTAAAGCGTCAT 59.806 34.615 18.40 11.41 39.24 3.06
3693 3938 7.128331 CGTGCCAAGATTAAGATAAGATTGTG 58.872 38.462 0.00 0.00 0.00 3.33
3826 4071 4.848357 TCTTGGCCTTCTCTTCTTAATGG 58.152 43.478 3.32 0.00 0.00 3.16
3831 4076 2.625639 TCCTCTTGGCCTTCTCTTCTT 58.374 47.619 3.32 0.00 0.00 2.52
3832 4077 2.334006 TCCTCTTGGCCTTCTCTTCT 57.666 50.000 3.32 0.00 0.00 2.85
3833 4078 2.916640 CATCCTCTTGGCCTTCTCTTC 58.083 52.381 3.32 0.00 0.00 2.87
3860 4105 5.877564 TCTGACACAACACAGAAAATACACA 59.122 36.000 0.00 0.00 39.68 3.72
3929 4177 3.725740 CACGATCAACAACACAAGCTTTC 59.274 43.478 0.00 0.00 0.00 2.62
3963 4211 6.347240 CGCATGAGGAGTAATAATTCAAGAGC 60.347 42.308 0.00 0.00 0.00 4.09
3964 4212 6.925718 TCGCATGAGGAGTAATAATTCAAGAG 59.074 38.462 0.00 0.00 0.00 2.85
3965 4213 6.816136 TCGCATGAGGAGTAATAATTCAAGA 58.184 36.000 0.00 0.00 0.00 3.02
3990 4238 6.773638 AGCCCATTACAGATAATTCTCGATT 58.226 36.000 0.00 0.00 0.00 3.34
3994 4242 7.807977 TGAAAGCCCATTACAGATAATTCTC 57.192 36.000 0.00 0.00 0.00 2.87
4013 4415 5.390461 CCAAATTTCACATGCATGCTGAAAG 60.390 40.000 34.28 27.35 39.13 2.62
4020 4422 8.929827 TCTAAATACCAAATTTCACATGCATG 57.070 30.769 25.09 25.09 0.00 4.06
4032 4434 9.606631 CTTCTAGAGTTGCTCTAAATACCAAAT 57.393 33.333 7.22 0.00 41.74 2.32
4033 4435 8.812972 TCTTCTAGAGTTGCTCTAAATACCAAA 58.187 33.333 7.22 0.00 41.74 3.28
4034 4436 8.251721 GTCTTCTAGAGTTGCTCTAAATACCAA 58.748 37.037 7.22 0.00 41.74 3.67
4035 4437 7.147880 GGTCTTCTAGAGTTGCTCTAAATACCA 60.148 40.741 17.68 0.26 41.74 3.25
4036 4438 7.068962 AGGTCTTCTAGAGTTGCTCTAAATACC 59.931 40.741 16.45 16.45 41.74 2.73
4037 4439 8.002984 AGGTCTTCTAGAGTTGCTCTAAATAC 57.997 38.462 7.22 7.30 41.74 1.89
4038 4440 7.012515 CGAGGTCTTCTAGAGTTGCTCTAAATA 59.987 40.741 7.22 0.00 41.74 1.40
4039 4441 6.183360 CGAGGTCTTCTAGAGTTGCTCTAAAT 60.183 42.308 7.22 0.00 41.74 1.40
4040 4442 5.124138 CGAGGTCTTCTAGAGTTGCTCTAAA 59.876 44.000 7.22 4.76 41.74 1.85
4041 4443 4.636648 CGAGGTCTTCTAGAGTTGCTCTAA 59.363 45.833 7.22 0.00 41.74 2.10
4042 4444 4.193090 CGAGGTCTTCTAGAGTTGCTCTA 58.807 47.826 5.84 5.84 41.50 2.43
4043 4445 3.013921 CGAGGTCTTCTAGAGTTGCTCT 58.986 50.000 4.02 4.02 43.83 4.09
4044 4446 2.478879 GCGAGGTCTTCTAGAGTTGCTC 60.479 54.545 0.00 0.00 0.00 4.26
4045 4447 1.474879 GCGAGGTCTTCTAGAGTTGCT 59.525 52.381 0.00 0.00 0.00 3.91
4046 4448 1.202582 TGCGAGGTCTTCTAGAGTTGC 59.797 52.381 0.00 0.00 0.00 4.17
4047 4449 3.577649 TTGCGAGGTCTTCTAGAGTTG 57.422 47.619 0.00 0.00 0.00 3.16
4048 4450 4.281182 TCTTTTGCGAGGTCTTCTAGAGTT 59.719 41.667 0.00 0.00 0.00 3.01
4049 4451 3.827302 TCTTTTGCGAGGTCTTCTAGAGT 59.173 43.478 0.00 0.00 0.00 3.24
4050 4452 4.170256 GTCTTTTGCGAGGTCTTCTAGAG 58.830 47.826 0.00 0.00 0.00 2.43
4051 4453 3.366070 CGTCTTTTGCGAGGTCTTCTAGA 60.366 47.826 0.00 0.00 0.00 2.43
4052 4454 2.917971 CGTCTTTTGCGAGGTCTTCTAG 59.082 50.000 0.00 0.00 0.00 2.43
4053 4455 2.925306 GCGTCTTTTGCGAGGTCTTCTA 60.925 50.000 0.00 0.00 0.00 2.10
4054 4456 1.784525 CGTCTTTTGCGAGGTCTTCT 58.215 50.000 0.00 0.00 0.00 2.85
4055 4457 0.164002 GCGTCTTTTGCGAGGTCTTC 59.836 55.000 0.00 0.00 0.00 2.87
4056 4458 2.235546 GCGTCTTTTGCGAGGTCTT 58.764 52.632 0.00 0.00 0.00 3.01
4057 4459 3.952811 GCGTCTTTTGCGAGGTCT 58.047 55.556 0.00 0.00 0.00 3.85
4064 4466 3.809990 CGGTTTCGCGTCTTTTGC 58.190 55.556 5.77 0.00 0.00 3.68
4081 4483 1.859998 GCATACTCGCCGGAATTTTGC 60.860 52.381 5.05 2.38 0.00 3.68
4082 4484 1.594518 CGCATACTCGCCGGAATTTTG 60.595 52.381 5.05 0.00 0.00 2.44
4083 4485 0.655733 CGCATACTCGCCGGAATTTT 59.344 50.000 5.05 0.00 0.00 1.82
4084 4486 1.157870 CCGCATACTCGCCGGAATTT 61.158 55.000 5.05 0.00 44.55 1.82
4085 4487 1.594293 CCGCATACTCGCCGGAATT 60.594 57.895 5.05 0.00 44.55 2.17
4086 4488 2.029073 CCGCATACTCGCCGGAAT 59.971 61.111 5.05 0.00 44.55 3.01
4087 4489 4.215742 CCCGCATACTCGCCGGAA 62.216 66.667 5.05 0.00 44.55 4.30
4094 4496 2.027751 GACCGAGCCCGCATACTC 59.972 66.667 0.00 0.00 0.00 2.59
4095 4497 3.537874 GGACCGAGCCCGCATACT 61.538 66.667 0.00 0.00 0.00 2.12
4096 4498 2.660258 ATTGGACCGAGCCCGCATAC 62.660 60.000 0.00 0.00 0.00 2.39
4097 4499 1.978455 AATTGGACCGAGCCCGCATA 61.978 55.000 0.00 0.00 0.00 3.14
4098 4500 2.837031 AAATTGGACCGAGCCCGCAT 62.837 55.000 0.00 0.00 0.00 4.73
4099 4501 3.561120 AAATTGGACCGAGCCCGCA 62.561 57.895 0.00 0.00 0.00 5.69
4100 4502 2.266376 GAAAATTGGACCGAGCCCGC 62.266 60.000 0.00 0.00 0.00 6.13
4101 4503 1.654023 GGAAAATTGGACCGAGCCCG 61.654 60.000 0.00 0.00 0.00 6.13
4102 4504 2.189833 GGAAAATTGGACCGAGCCC 58.810 57.895 0.00 0.00 0.00 5.19
4107 4509 1.933115 CTGGCCGGAAAATTGGACCG 61.933 60.000 5.28 10.06 45.24 4.79
4108 4510 0.610785 TCTGGCCGGAAAATTGGACC 60.611 55.000 13.31 0.00 29.51 4.46
4109 4511 1.067846 GTTCTGGCCGGAAAATTGGAC 60.068 52.381 28.65 11.55 0.00 4.02
4110 4512 1.253100 GTTCTGGCCGGAAAATTGGA 58.747 50.000 28.65 1.55 0.00 3.53
4111 4513 0.965439 TGTTCTGGCCGGAAAATTGG 59.035 50.000 28.65 0.00 0.00 3.16
4112 4514 2.810439 TTGTTCTGGCCGGAAAATTG 57.190 45.000 28.65 0.00 0.00 2.32
4113 4515 2.547855 GCTTTGTTCTGGCCGGAAAATT 60.548 45.455 28.65 0.00 0.00 1.82
4114 4516 1.000843 GCTTTGTTCTGGCCGGAAAAT 59.999 47.619 28.65 0.00 0.00 1.82
4115 4517 0.387565 GCTTTGTTCTGGCCGGAAAA 59.612 50.000 28.65 21.44 0.00 2.29
4116 4518 1.460273 GGCTTTGTTCTGGCCGGAAA 61.460 55.000 28.65 15.66 36.37 3.13
4117 4519 1.901464 GGCTTTGTTCTGGCCGGAA 60.901 57.895 23.60 23.60 36.37 4.30
4118 4520 2.282180 GGCTTTGTTCTGGCCGGA 60.282 61.111 11.27 11.27 36.37 5.14
4121 4523 1.538687 ATGCTGGCTTTGTTCTGGCC 61.539 55.000 0.00 0.00 45.45 5.36
4122 4524 1.135286 GTATGCTGGCTTTGTTCTGGC 60.135 52.381 0.00 0.00 0.00 4.85
4123 4525 2.421424 GAGTATGCTGGCTTTGTTCTGG 59.579 50.000 0.00 0.00 0.00 3.86
4124 4526 2.094894 CGAGTATGCTGGCTTTGTTCTG 59.905 50.000 0.00 0.00 0.00 3.02
4125 4527 2.350522 CGAGTATGCTGGCTTTGTTCT 58.649 47.619 0.00 0.00 0.00 3.01
4126 4528 1.202076 GCGAGTATGCTGGCTTTGTTC 60.202 52.381 10.48 0.00 42.19 3.18
4127 4529 0.804989 GCGAGTATGCTGGCTTTGTT 59.195 50.000 10.48 0.00 42.19 2.83
4128 4530 1.026718 GGCGAGTATGCTGGCTTTGT 61.027 55.000 16.65 0.00 44.41 2.83
4129 4531 1.718757 GGGCGAGTATGCTGGCTTTG 61.719 60.000 16.65 0.00 44.41 2.77
4130 4532 1.452108 GGGCGAGTATGCTGGCTTT 60.452 57.895 16.65 0.00 44.41 3.51
4131 4533 2.190578 GGGCGAGTATGCTGGCTT 59.809 61.111 16.65 0.00 44.41 4.35
4132 4534 3.866582 GGGGCGAGTATGCTGGCT 61.867 66.667 16.65 0.00 44.41 4.75
4139 4541 4.900704 TACGGGCGGGGCGAGTAT 62.901 66.667 0.00 0.00 0.00 2.12
4142 4544 4.763646 TTTTACGGGCGGGGCGAG 62.764 66.667 0.00 0.00 0.00 5.03
4143 4545 4.763646 CTTTTACGGGCGGGGCGA 62.764 66.667 0.00 0.00 0.00 5.54
4144 4546 4.763646 TCTTTTACGGGCGGGGCG 62.764 66.667 0.00 0.00 0.00 6.13
4145 4547 1.317431 AATTCTTTTACGGGCGGGGC 61.317 55.000 0.00 0.00 0.00 5.80
4146 4548 1.135228 CAAATTCTTTTACGGGCGGGG 60.135 52.381 0.00 0.00 0.00 5.73
4147 4549 1.734377 GCAAATTCTTTTACGGGCGGG 60.734 52.381 0.00 0.00 0.00 6.13
4148 4550 1.624487 GCAAATTCTTTTACGGGCGG 58.376 50.000 0.00 0.00 0.00 6.13
4149 4551 1.624487 GGCAAATTCTTTTACGGGCG 58.376 50.000 0.00 0.00 0.00 6.13
4150 4552 1.624487 CGGCAAATTCTTTTACGGGC 58.376 50.000 0.00 0.00 0.00 6.13
4151 4553 1.624487 GCGGCAAATTCTTTTACGGG 58.376 50.000 0.00 0.00 0.00 5.28
4152 4554 1.255767 CGCGGCAAATTCTTTTACGG 58.744 50.000 0.00 0.00 0.00 4.02
4153 4555 1.255767 CCGCGGCAAATTCTTTTACG 58.744 50.000 14.67 0.00 0.00 3.18
4154 4556 0.989164 GCCGCGGCAAATTCTTTTAC 59.011 50.000 43.55 10.27 41.49 2.01
4155 4557 0.109039 GGCCGCGGCAAATTCTTTTA 60.109 50.000 46.88 0.00 44.11 1.52
4156 4558 1.374125 GGCCGCGGCAAATTCTTTT 60.374 52.632 46.88 0.00 44.11 2.27
4157 4559 2.261361 GGCCGCGGCAAATTCTTT 59.739 55.556 46.88 0.00 44.11 2.52
4158 4560 2.676471 AGGCCGCGGCAAATTCTT 60.676 55.556 46.88 22.12 44.11 2.52
4159 4561 3.443045 CAGGCCGCGGCAAATTCT 61.443 61.111 46.88 32.77 44.11 2.40
4176 4578 3.372730 TCGGGGCATGCAGTTTGC 61.373 61.111 21.36 2.03 45.29 3.68
4177 4579 2.568090 GTCGGGGCATGCAGTTTG 59.432 61.111 21.36 4.15 0.00 2.93
4178 4580 2.676471 GGTCGGGGCATGCAGTTT 60.676 61.111 21.36 0.00 0.00 2.66
4179 4581 3.965258 TGGTCGGGGCATGCAGTT 61.965 61.111 21.36 0.00 0.00 3.16
4180 4582 4.722700 GTGGTCGGGGCATGCAGT 62.723 66.667 21.36 0.00 0.00 4.40
4181 4583 2.329539 ATAGTGGTCGGGGCATGCAG 62.330 60.000 21.36 10.35 0.00 4.41
4182 4584 1.051556 TATAGTGGTCGGGGCATGCA 61.052 55.000 21.36 0.00 0.00 3.96
4183 4585 0.324943 ATATAGTGGTCGGGGCATGC 59.675 55.000 9.90 9.90 0.00 4.06
4184 4586 1.902508 AGATATAGTGGTCGGGGCATG 59.097 52.381 0.00 0.00 0.00 4.06
4185 4587 2.327325 AGATATAGTGGTCGGGGCAT 57.673 50.000 0.00 0.00 0.00 4.40
4186 4588 2.522185 GTAGATATAGTGGTCGGGGCA 58.478 52.381 0.00 0.00 0.00 5.36
4187 4589 1.471684 CGTAGATATAGTGGTCGGGGC 59.528 57.143 0.00 0.00 0.00 5.80
4188 4590 2.089980 CCGTAGATATAGTGGTCGGGG 58.910 57.143 0.00 0.00 34.05 5.73
4189 4591 2.787994 ACCGTAGATATAGTGGTCGGG 58.212 52.381 0.00 0.00 40.60 5.14
4190 4592 4.416505 GAACCGTAGATATAGTGGTCGG 57.583 50.000 0.00 0.00 41.77 4.79


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

AutoCloner maintained by Alex Coulton.