Multiple sequence alignment - TraesCS5A01G134600

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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 TraesCS5A01G134600 chr5A 100.000 4269 0 0 1 4269 303399213 303403481 0.000000e+00 7884.0
1 TraesCS5A01G134600 chr5A 92.763 152 11 0 598 749 335291434 335291585 2.000000e-53 220.0
2 TraesCS5A01G134600 chr5A 96.923 65 1 1 4061 4125 303403221 303403284 1.620000e-19 108.0
3 TraesCS5A01G134600 chr5A 96.923 65 1 1 4009 4072 303403273 303403337 1.620000e-19 108.0
4 TraesCS5A01G134600 chr5D 94.931 4182 124 37 1 4133 221150151 221146009 0.000000e+00 6468.0
5 TraesCS5A01G134600 chr5D 93.960 149 9 0 601 749 256749951 256749803 4.300000e-55 226.0
6 TraesCS5A01G134600 chr5D 97.297 37 1 0 4036 4072 221146053 221146017 3.560000e-06 63.9
7 TraesCS5A01G134600 chr5D 100.000 28 0 0 3935 3962 386888223 386888250 8.000000e-03 52.8
8 TraesCS5A01G134600 chr5B 95.976 3106 86 12 884 3962 243850746 243847653 0.000000e+00 5007.0
9 TraesCS5A01G134600 chr5B 95.280 911 32 3 1 904 243851770 243850864 0.000000e+00 1434.0
10 TraesCS5A01G134600 chr7B 97.656 128 3 0 4142 4269 590441541 590441414 2.000000e-53 220.0
11 TraesCS5A01G134600 chr7B 92.258 155 10 2 600 752 59069210 59069364 7.190000e-53 219.0
12 TraesCS5A01G134600 chr7B 96.875 128 4 0 4142 4269 713593402 713593529 9.300000e-52 215.0
13 TraesCS5A01G134600 chr7B 96.875 128 4 0 4142 4269 732302639 732302766 9.300000e-52 215.0
14 TraesCS5A01G134600 chr7B 96.094 128 5 0 4142 4269 110111874 110111747 4.330000e-50 209.0
15 TraesCS5A01G134600 chr4B 92.258 155 10 2 595 748 106227403 106227556 7.190000e-53 219.0
16 TraesCS5A01G134600 chr4B 92.208 154 11 1 601 754 78607919 78607767 2.580000e-52 217.0
17 TraesCS5A01G134600 chr4B 96.094 128 5 0 4142 4269 141251529 141251656 4.330000e-50 209.0
18 TraesCS5A01G134600 chr4B 100.000 28 0 0 3935 3962 564650732 564650705 8.000000e-03 52.8
19 TraesCS5A01G134600 chr2A 93.289 149 8 2 601 748 141506470 141506323 7.190000e-53 219.0
20 TraesCS5A01G134600 chr2B 91.304 161 11 3 594 754 251374806 251374963 2.580000e-52 217.0
21 TraesCS5A01G134600 chr2B 96.094 128 4 1 4142 4269 454345723 454345597 1.560000e-49 207.0
22 TraesCS5A01G134600 chrUn 96.094 128 5 0 4142 4269 475524723 475524850 4.330000e-50 209.0
23 TraesCS5A01G134600 chrUn 100.000 28 0 0 3935 3962 363028882 363028855 8.000000e-03 52.8
24 TraesCS5A01G134600 chrUn 100.000 28 0 0 3935 3962 397311069 397311096 8.000000e-03 52.8
25 TraesCS5A01G134600 chr3B 96.094 128 5 0 4142 4269 752858661 752858534 4.330000e-50 209.0
26 TraesCS5A01G134600 chr3B 96.094 128 5 0 4142 4269 819310286 819310159 4.330000e-50 209.0
27 TraesCS5A01G134600 chr7D 100.000 29 0 0 3935 3963 543607993 543607965 2.000000e-03 54.7
28 TraesCS5A01G134600 chr3D 100.000 28 0 0 3935 3962 579233590 579233563 8.000000e-03 52.8
29 TraesCS5A01G134600 chr2D 100.000 28 0 0 3935 3962 18147867 18147840 8.000000e-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 TraesCS5A01G134600 chr5A 303399213 303403481 4268 False 2700.0 7884 97.948667 1 4269 3 chr5A.!!$F2 4268
1 TraesCS5A01G134600 chr5D 221146009 221150151 4142 True 6468.0 6468 94.931000 1 4133 1 chr5D.!!$R1 4132
2 TraesCS5A01G134600 chr5B 243847653 243851770 4117 True 3220.5 5007 95.628000 1 3962 2 chr5B.!!$R1 3961

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
589 597 0.538118 CTGTCCGTCCGGGGAATAAA 59.462 55.000 0.00 0.0 37.96 1.40 F
859 867 2.772739 ATGCTTGCCATGAGTCGTC 58.227 52.632 0.00 0.0 31.48 4.20 F
1699 1845 3.678289 TGTTGTCTTATGTGCTGCAGAT 58.322 40.909 20.43 16.8 0.00 2.90 F
2089 2237 0.477795 AAAACTGTAGGGGAGGGGCT 60.478 55.000 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1754 2.439507 GCATACCTGGATCTCCCTTTCA 59.560 50.000 0.00 0.0 35.38 2.69 R
2064 2212 3.181433 CCCTCCCCTACAGTTTTCAGTTT 60.181 47.826 0.00 0.0 0.00 2.66 R
2881 3029 1.432270 GCGGGTGCAGCTAAGTGATC 61.432 60.000 16.65 0.0 42.15 2.92 R
3962 4153 1.525077 GAGTGTGCCGGTTGTGGAA 60.525 57.895 1.90 0.0 0.00 3.53 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
72 73 2.841988 GGATCTCAGCCTCCGCCT 60.842 66.667 0.00 0.00 34.57 5.52
156 157 2.339556 TTGGGAATTCAAGGCCGCG 61.340 57.895 7.93 0.00 0.00 6.46
249 250 2.838202 TGTTCCTGTAGTGATCCCTTCC 59.162 50.000 0.00 0.00 0.00 3.46
392 400 3.772853 TAGGGCATGTGCGGGATGC 62.773 63.158 5.97 5.97 44.65 3.91
446 454 6.349363 CCAAAGCTAACCCACTGTAGAAAATC 60.349 42.308 0.00 0.00 0.00 2.17
462 470 2.886730 AATCCGTTGCTAAGCCCCGG 62.887 60.000 0.00 0.00 40.47 5.73
558 566 9.144298 CAGACTACTTCAAGGGGTAATATTCTA 57.856 37.037 0.00 0.00 0.00 2.10
579 587 1.276989 TCCCATGTAAACTGTCCGTCC 59.723 52.381 0.00 0.00 0.00 4.79
589 597 0.538118 CTGTCCGTCCGGGGAATAAA 59.462 55.000 0.00 0.00 37.96 1.40
620 628 6.906901 ACTAGTACTCCCTCCATTCCAAATTA 59.093 38.462 0.00 0.00 0.00 1.40
750 758 5.850614 TCTTATAATTAGGAACGGAGGTGC 58.149 41.667 0.00 0.00 0.00 5.01
766 774 4.383118 GGAGGTGCATAAAGCTCTAACTCA 60.383 45.833 0.00 0.00 45.94 3.41
812 820 7.206981 AGACTTGGACATTAATTCAGTGTTG 57.793 36.000 0.00 0.00 0.00 3.33
859 867 2.772739 ATGCTTGCCATGAGTCGTC 58.227 52.632 0.00 0.00 31.48 4.20
975 1121 3.891977 CCTTCTCCTGATCTGGTTCGATA 59.108 47.826 17.33 0.00 0.00 2.92
1253 1399 7.509141 TCAGCTCTTCTGATATGTTCTCTAG 57.491 40.000 0.00 0.00 46.34 2.43
1303 1449 7.771826 GGTATTTTAAGTTACCAGTGGATAGCA 59.228 37.037 18.40 0.00 38.20 3.49
1306 1452 7.859325 TTTAAGTTACCAGTGGATAGCATTC 57.141 36.000 18.40 0.00 0.00 2.67
1699 1845 3.678289 TGTTGTCTTATGTGCTGCAGAT 58.322 40.909 20.43 16.80 0.00 2.90
1839 1985 4.526262 CGAGGGATGAGAGTATTTCTGGAT 59.474 45.833 0.00 0.00 35.87 3.41
2010 2156 4.207955 ACTCATCCTACTGTTATCAGCGA 58.792 43.478 0.51 0.00 44.77 4.93
2089 2237 0.477795 AAAACTGTAGGGGAGGGGCT 60.478 55.000 0.00 0.00 0.00 5.19
2240 2388 3.274288 CACCATTCTTACCCTCTGAAGC 58.726 50.000 0.00 0.00 0.00 3.86
2567 2715 4.171754 GCTTTGGCAAGAATCTTGTCATC 58.828 43.478 27.90 17.07 33.68 2.92
2568 2716 4.082354 GCTTTGGCAAGAATCTTGTCATCT 60.082 41.667 27.90 0.00 33.68 2.90
2618 2766 6.878923 TGAAGGTACAGATGTTTCGATCAATT 59.121 34.615 0.00 0.00 0.00 2.32
2619 2767 7.390440 TGAAGGTACAGATGTTTCGATCAATTT 59.610 33.333 0.00 0.00 0.00 1.82
2881 3029 4.904116 TCTTAAAACAGTTGTTGACAGCG 58.096 39.130 0.00 0.00 38.44 5.18
2926 3074 1.110442 AGCTCTTCTGGAGTCCATCG 58.890 55.000 13.56 1.62 43.62 3.84
2947 3095 6.887376 TCGTCAGTATTAATGAACTTGAGC 57.113 37.500 0.00 0.00 0.00 4.26
2959 3107 2.825861 ACTTGAGCTGGCCAATTTTG 57.174 45.000 7.01 0.00 0.00 2.44
2963 3111 1.000385 TGAGCTGGCCAATTTTGAACG 60.000 47.619 7.01 0.00 0.00 3.95
3019 3167 0.846693 ACTCCTGCCAACTGGTCTTT 59.153 50.000 0.00 0.00 36.34 2.52
3239 3387 5.567234 CGTTCATATCTCTTCAATGGACG 57.433 43.478 1.41 1.41 43.79 4.79
3264 3412 2.196319 GCAATAGCTGCCTGCCTTT 58.804 52.632 0.00 0.00 46.13 3.11
3341 3492 2.885135 TCCAGTGGAAGCATCACAAT 57.115 45.000 10.20 0.00 37.58 2.71
3374 3525 4.858692 CCAAAACTTATTCATGAGGTTGCG 59.141 41.667 0.00 0.00 0.00 4.85
3451 3611 2.890808 TCAATCCATGGAGACTACGC 57.109 50.000 21.33 0.00 0.00 4.42
3699 3859 5.903010 TGGTCCTGCCAGTTCTAGATTTATA 59.097 40.000 0.00 0.00 43.61 0.98
3816 3982 3.959535 ACAACCACAATGGGCTAATTG 57.040 42.857 10.57 10.57 43.37 2.32
3857 4047 0.616891 GGGTTATATGCCCGGGTAGG 59.383 60.000 24.63 0.00 36.30 3.18
3926 4117 7.987458 TGATTAGACATTTCATCAAGTACTCCC 59.013 37.037 0.00 0.00 0.00 4.30
3937 4128 7.363031 TCATCAAGTACTCCCTCTATAACCTT 58.637 38.462 0.00 0.00 0.00 3.50
3944 4135 8.979534 AGTACTCCCTCTATAACCTTTGTAAAG 58.020 37.037 0.00 0.00 35.79 1.85
3999 4211 0.097674 CGTTGGCTGCATGAACTAGC 59.902 55.000 0.50 0.00 36.74 3.42
4001 4213 1.135575 GTTGGCTGCATGAACTAGCAC 60.136 52.381 0.50 0.00 39.15 4.40
4004 4216 1.346197 CTGCATGAACTAGCACGCG 59.654 57.895 3.53 3.53 36.62 6.01
4040 4291 4.595538 AACCAGCGACGGCGTCAA 62.596 61.111 35.62 0.00 46.35 3.18
4104 4355 4.156622 CGTCAGTCGTAGCCGCGA 62.157 66.667 8.23 0.00 38.68 5.87
4105 4356 2.277373 GTCAGTCGTAGCCGCGAG 60.277 66.667 8.23 0.00 41.85 5.03
4106 4357 2.435410 TCAGTCGTAGCCGCGAGA 60.435 61.111 8.23 0.00 41.85 4.04
4107 4358 1.818363 TCAGTCGTAGCCGCGAGAT 60.818 57.895 8.23 0.00 41.85 2.75
4108 4359 1.064296 CAGTCGTAGCCGCGAGATT 59.936 57.895 8.23 0.00 41.85 2.40
4109 4360 0.930742 CAGTCGTAGCCGCGAGATTC 60.931 60.000 8.23 0.00 41.85 2.52
4110 4361 1.063649 GTCGTAGCCGCGAGATTCA 59.936 57.895 8.23 0.00 41.85 2.57
4111 4362 0.930742 GTCGTAGCCGCGAGATTCAG 60.931 60.000 8.23 0.00 41.85 3.02
4112 4363 1.658717 CGTAGCCGCGAGATTCAGG 60.659 63.158 8.23 0.00 0.00 3.86
4113 4364 1.300233 GTAGCCGCGAGATTCAGGG 60.300 63.158 8.23 0.00 0.00 4.45
4114 4365 2.498941 TAGCCGCGAGATTCAGGGG 61.499 63.158 8.23 9.78 42.55 4.79
4116 4367 4.161295 CCGCGAGATTCAGGGGCA 62.161 66.667 8.23 0.00 33.73 5.36
4117 4368 2.587194 CGCGAGATTCAGGGGCAG 60.587 66.667 0.00 0.00 0.00 4.85
4118 4369 2.203126 GCGAGATTCAGGGGCAGG 60.203 66.667 0.00 0.00 0.00 4.85
4119 4370 2.507944 CGAGATTCAGGGGCAGGG 59.492 66.667 0.00 0.00 0.00 4.45
4120 4371 2.194326 GAGATTCAGGGGCAGGGC 59.806 66.667 0.00 0.00 0.00 5.19
4121 4372 2.286732 AGATTCAGGGGCAGGGCT 60.287 61.111 0.00 0.00 0.00 5.19
4122 4373 2.123982 GATTCAGGGGCAGGGCTG 60.124 66.667 0.00 0.00 0.00 4.85
4145 4396 4.696805 GGCGGGGCCTTTTCCCTT 62.697 66.667 0.84 0.00 46.69 3.95
4146 4397 2.603473 GCGGGGCCTTTTCCCTTT 60.603 61.111 0.84 0.00 45.80 3.11
4147 4398 2.942796 GCGGGGCCTTTTCCCTTTG 61.943 63.158 0.84 0.00 45.80 2.77
4148 4399 1.228737 CGGGGCCTTTTCCCTTTGA 60.229 57.895 0.84 0.00 45.80 2.69
4149 4400 0.830023 CGGGGCCTTTTCCCTTTGAA 60.830 55.000 0.84 0.00 45.80 2.69
4150 4401 0.685097 GGGGCCTTTTCCCTTTGAAC 59.315 55.000 0.84 0.00 45.80 3.18
4151 4402 0.317160 GGGCCTTTTCCCTTTGAACG 59.683 55.000 0.84 0.00 43.13 3.95
4152 4403 1.324383 GGCCTTTTCCCTTTGAACGA 58.676 50.000 0.00 0.00 31.05 3.85
4153 4404 1.684450 GGCCTTTTCCCTTTGAACGAA 59.316 47.619 0.00 0.00 31.05 3.85
4154 4405 2.545113 GGCCTTTTCCCTTTGAACGAAC 60.545 50.000 0.00 0.00 31.05 3.95
4155 4406 2.361119 GCCTTTTCCCTTTGAACGAACT 59.639 45.455 0.00 0.00 31.05 3.01
4156 4407 3.181479 GCCTTTTCCCTTTGAACGAACTT 60.181 43.478 0.00 0.00 31.05 2.66
4157 4408 4.679639 GCCTTTTCCCTTTGAACGAACTTT 60.680 41.667 0.00 0.00 31.05 2.66
4158 4409 4.803613 CCTTTTCCCTTTGAACGAACTTTG 59.196 41.667 0.00 0.00 31.05 2.77
4159 4410 5.394224 TTTTCCCTTTGAACGAACTTTGT 57.606 34.783 0.00 0.00 31.05 2.83
4160 4411 4.625972 TTCCCTTTGAACGAACTTTGTC 57.374 40.909 0.00 0.00 0.00 3.18
4161 4412 3.611970 TCCCTTTGAACGAACTTTGTCA 58.388 40.909 0.00 0.00 0.00 3.58
4162 4413 3.375922 TCCCTTTGAACGAACTTTGTCAC 59.624 43.478 0.00 0.00 0.00 3.67
4163 4414 3.127895 CCCTTTGAACGAACTTTGTCACA 59.872 43.478 0.00 0.00 0.00 3.58
4164 4415 4.380023 CCCTTTGAACGAACTTTGTCACAA 60.380 41.667 0.00 0.00 0.00 3.33
4165 4416 5.157781 CCTTTGAACGAACTTTGTCACAAA 58.842 37.500 2.24 2.24 0.00 2.83
4166 4417 5.631512 CCTTTGAACGAACTTTGTCACAAAA 59.368 36.000 4.13 0.00 30.94 2.44
4167 4418 6.310224 CCTTTGAACGAACTTTGTCACAAAAT 59.690 34.615 4.13 0.00 30.94 1.82
4168 4419 6.624710 TTGAACGAACTTTGTCACAAAATG 57.375 33.333 4.13 0.00 0.00 2.32
4169 4420 5.944013 TGAACGAACTTTGTCACAAAATGA 58.056 33.333 4.13 0.00 33.79 2.57
4170 4421 6.382608 TGAACGAACTTTGTCACAAAATGAA 58.617 32.000 4.13 0.00 39.72 2.57
4171 4422 7.032580 TGAACGAACTTTGTCACAAAATGAAT 58.967 30.769 4.13 0.00 39.72 2.57
4172 4423 7.543868 TGAACGAACTTTGTCACAAAATGAATT 59.456 29.630 4.13 0.00 39.72 2.17
4173 4424 7.449934 ACGAACTTTGTCACAAAATGAATTC 57.550 32.000 4.13 0.00 39.72 2.17
4174 4425 6.196353 ACGAACTTTGTCACAAAATGAATTCG 59.804 34.615 20.45 20.45 39.72 3.34
4175 4426 6.413526 CGAACTTTGTCACAAAATGAATTCGA 59.586 34.615 18.83 0.00 39.72 3.71
4176 4427 7.449934 AACTTTGTCACAAAATGAATTCGAC 57.550 32.000 4.13 1.05 39.72 4.20
4177 4428 5.681105 ACTTTGTCACAAAATGAATTCGACG 59.319 36.000 4.13 0.00 39.72 5.12
4178 4429 4.804608 TGTCACAAAATGAATTCGACGT 57.195 36.364 0.04 0.00 39.72 4.34
4179 4430 4.522877 TGTCACAAAATGAATTCGACGTG 58.477 39.130 0.00 4.28 39.72 4.49
4180 4431 4.271291 TGTCACAAAATGAATTCGACGTGA 59.729 37.500 0.00 6.46 39.72 4.35
4181 4432 5.201910 GTCACAAAATGAATTCGACGTGAA 58.798 37.500 13.92 0.00 39.72 3.18
4182 4433 5.679355 GTCACAAAATGAATTCGACGTGAAA 59.321 36.000 13.92 0.00 39.72 2.69
4183 4434 5.906838 TCACAAAATGAATTCGACGTGAAAG 59.093 36.000 0.00 0.00 34.20 2.62
4184 4435 5.681105 CACAAAATGAATTCGACGTGAAAGT 59.319 36.000 0.00 0.00 40.71 2.66
4185 4436 6.848800 CACAAAATGAATTCGACGTGAAAGTA 59.151 34.615 0.00 0.00 40.71 2.24
4186 4437 7.533900 CACAAAATGAATTCGACGTGAAAGTAT 59.466 33.333 0.00 0.00 40.71 2.12
4187 4438 8.073768 ACAAAATGAATTCGACGTGAAAGTATT 58.926 29.630 0.00 0.00 40.71 1.89
4188 4439 8.901748 CAAAATGAATTCGACGTGAAAGTATTT 58.098 29.630 0.00 3.83 43.98 1.40
4205 4456 8.655935 AAAGTATTTCATGATCTGACCCTTTT 57.344 30.769 0.00 0.00 27.08 2.27
4206 4457 9.753674 AAAGTATTTCATGATCTGACCCTTTTA 57.246 29.630 0.00 0.00 27.08 1.52
4207 4458 8.970859 AGTATTTCATGATCTGACCCTTTTAG 57.029 34.615 0.00 0.00 32.17 1.85
4208 4459 6.705863 ATTTCATGATCTGACCCTTTTAGC 57.294 37.500 0.00 0.00 32.17 3.09
4209 4460 4.842531 TCATGATCTGACCCTTTTAGCA 57.157 40.909 0.00 0.00 0.00 3.49
4210 4461 5.178096 TCATGATCTGACCCTTTTAGCAA 57.822 39.130 0.00 0.00 0.00 3.91
4211 4462 5.759059 TCATGATCTGACCCTTTTAGCAAT 58.241 37.500 0.00 0.00 0.00 3.56
4212 4463 5.591472 TCATGATCTGACCCTTTTAGCAATG 59.409 40.000 0.00 0.00 0.00 2.82
4213 4464 3.696051 TGATCTGACCCTTTTAGCAATGC 59.304 43.478 0.00 0.00 0.00 3.56
4214 4465 2.446435 TCTGACCCTTTTAGCAATGCC 58.554 47.619 0.00 0.00 0.00 4.40
4215 4466 2.170166 CTGACCCTTTTAGCAATGCCA 58.830 47.619 0.00 0.00 0.00 4.92
4216 4467 1.892474 TGACCCTTTTAGCAATGCCAC 59.108 47.619 0.00 0.00 0.00 5.01
4217 4468 1.892474 GACCCTTTTAGCAATGCCACA 59.108 47.619 0.00 0.00 0.00 4.17
4218 4469 1.895131 ACCCTTTTAGCAATGCCACAG 59.105 47.619 0.00 0.00 0.00 3.66
4219 4470 1.404583 CCCTTTTAGCAATGCCACAGC 60.405 52.381 0.00 0.00 40.48 4.40
4220 4471 1.404583 CCTTTTAGCAATGCCACAGCC 60.405 52.381 0.00 0.00 38.69 4.85
4221 4472 0.607620 TTTTAGCAATGCCACAGCCC 59.392 50.000 0.00 0.00 38.69 5.19
4222 4473 1.594194 TTTAGCAATGCCACAGCCCG 61.594 55.000 0.00 0.00 38.69 6.13
4243 4494 3.996825 GCGTTTCTGCCCAACATAG 57.003 52.632 0.00 0.00 0.00 2.23
4244 4495 1.448985 GCGTTTCTGCCCAACATAGA 58.551 50.000 0.00 0.00 0.00 1.98
4245 4496 1.810151 GCGTTTCTGCCCAACATAGAA 59.190 47.619 0.00 0.00 0.00 2.10
4246 4497 2.227865 GCGTTTCTGCCCAACATAGAAA 59.772 45.455 0.00 0.00 37.91 2.52
4248 4499 3.821841 GTTTCTGCCCAACATAGAAACG 58.178 45.455 11.75 0.00 45.66 3.60
4249 4500 1.448985 TCTGCCCAACATAGAAACGC 58.551 50.000 0.00 0.00 0.00 4.84
4250 4501 0.451783 CTGCCCAACATAGAAACGCC 59.548 55.000 0.00 0.00 0.00 5.68
4251 4502 1.302383 TGCCCAACATAGAAACGCCG 61.302 55.000 0.00 0.00 0.00 6.46
4252 4503 1.022451 GCCCAACATAGAAACGCCGA 61.022 55.000 0.00 0.00 0.00 5.54
4253 4504 1.006832 CCCAACATAGAAACGCCGAG 58.993 55.000 0.00 0.00 0.00 4.63
4254 4505 1.006832 CCAACATAGAAACGCCGAGG 58.993 55.000 0.00 0.00 0.00 4.63
4255 4506 1.674817 CCAACATAGAAACGCCGAGGT 60.675 52.381 0.00 0.00 0.00 3.85
4256 4507 2.417651 CCAACATAGAAACGCCGAGGTA 60.418 50.000 0.00 0.00 0.00 3.08
4257 4508 2.858344 CAACATAGAAACGCCGAGGTAG 59.142 50.000 0.00 0.00 0.00 3.18
4258 4509 1.202382 ACATAGAAACGCCGAGGTAGC 60.202 52.381 0.00 0.00 0.00 3.58
4259 4510 1.067212 CATAGAAACGCCGAGGTAGCT 59.933 52.381 0.00 0.00 0.00 3.32
4260 4511 2.042686 TAGAAACGCCGAGGTAGCTA 57.957 50.000 0.00 0.00 0.00 3.32
4261 4512 0.739561 AGAAACGCCGAGGTAGCTAG 59.260 55.000 0.00 0.00 0.00 3.42
4262 4513 0.870735 GAAACGCCGAGGTAGCTAGC 60.871 60.000 15.19 15.19 0.00 3.42
4264 4515 3.584052 CGCCGAGGTAGCTAGCGT 61.584 66.667 23.49 6.00 41.78 5.07
4265 4516 2.806237 GCCGAGGTAGCTAGCGTT 59.194 61.111 16.82 0.54 0.00 4.84
4266 4517 1.141234 GCCGAGGTAGCTAGCGTTT 59.859 57.895 16.82 0.00 0.00 3.60
4267 4518 0.870735 GCCGAGGTAGCTAGCGTTTC 60.871 60.000 16.82 8.69 0.00 2.78
4268 4519 0.739561 CCGAGGTAGCTAGCGTTTCT 59.260 55.000 16.82 5.87 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 157 4.247380 CCGGCATCAGAGGAGGGC 62.247 72.222 0.00 0.00 45.73 5.19
249 250 9.346725 GAAAATTTACAAAGACAGCTATGAAGG 57.653 33.333 0.00 0.00 0.00 3.46
358 366 2.355209 GCCCTACTTCACAAGCTAGCTT 60.355 50.000 24.42 24.42 36.60 3.74
392 400 9.657121 GCTAGCAGCAAATTAGTAAGAAATAAG 57.343 33.333 10.63 0.00 41.89 1.73
462 470 2.889852 CTCTTAGGTTACAGTTCCGGC 58.110 52.381 0.00 0.00 0.00 6.13
509 517 5.982516 TGATTGTTTTACTGAATTGCCACAC 59.017 36.000 0.00 0.00 0.00 3.82
520 528 8.499162 CCTTGAAGTAGTCTGATTGTTTTACTG 58.501 37.037 0.00 0.00 0.00 2.74
558 566 2.093128 GGACGGACAGTTTACATGGGAT 60.093 50.000 0.00 0.00 0.00 3.85
574 582 0.251073 ACACTTTATTCCCCGGACGG 59.749 55.000 0.73 3.25 0.00 4.79
579 587 7.105241 AGTACTAGTTACACTTTATTCCCCG 57.895 40.000 0.00 0.00 32.41 5.73
589 597 4.942363 TGGAGGGAGTACTAGTTACACT 57.058 45.455 0.00 0.00 32.41 3.55
662 670 5.179742 TGAGTGAACAAACACACTAAAACGT 59.820 36.000 0.00 0.00 45.54 3.99
750 758 6.166279 TGAAGGTGTGAGTTAGAGCTTTATG 58.834 40.000 0.00 0.00 40.08 1.90
766 774 8.603304 AGTCTAAAACTATAACCATGAAGGTGT 58.397 33.333 0.00 0.00 43.60 4.16
819 827 6.377146 GCATGACCTCCATTTTTACTAGGAAA 59.623 38.462 0.00 0.00 31.94 3.13
873 881 7.941238 AGCCTTAAGAGGTATATGTTCGTAGTA 59.059 37.037 3.36 0.00 45.44 1.82
874 882 6.776603 AGCCTTAAGAGGTATATGTTCGTAGT 59.223 38.462 3.36 0.00 45.44 2.73
875 883 7.175293 AGAGCCTTAAGAGGTATATGTTCGTAG 59.825 40.741 3.36 0.00 45.44 3.51
878 886 6.016192 TCAGAGCCTTAAGAGGTATATGTTCG 60.016 42.308 3.36 0.00 45.44 3.95
1253 1399 5.627499 TGAAATACTCACCACTTCATTGC 57.373 39.130 0.00 0.00 0.00 3.56
1301 1447 7.298507 AGCACACATCAAAATAAATGAATGC 57.701 32.000 0.00 0.00 37.45 3.56
1608 1754 2.439507 GCATACCTGGATCTCCCTTTCA 59.560 50.000 0.00 0.00 35.38 2.69
1839 1985 5.298989 TCCTCTTTGGTACTGTTAAGCAA 57.701 39.130 0.00 0.00 37.07 3.91
1938 2084 9.503427 TGATAACGAGCAGATAATTACATATCG 57.497 33.333 0.00 7.14 37.37 2.92
1987 2133 4.645136 TCGCTGATAACAGTAGGATGAGTT 59.355 41.667 1.65 0.00 45.04 3.01
2010 2156 5.075493 AGAATGATCTGTGCCAGTCTTTTT 58.925 37.500 0.00 0.00 34.55 1.94
2064 2212 3.181433 CCCTCCCCTACAGTTTTCAGTTT 60.181 47.826 0.00 0.00 0.00 2.66
2089 2237 6.037786 ACTGATCTTGATTTTACTGTCGGA 57.962 37.500 0.00 0.00 0.00 4.55
2379 2527 4.999311 TCATGTCATGCTGTGCCTATATTC 59.001 41.667 8.03 0.00 0.00 1.75
2490 2638 4.465632 AGAAACATACTGTACCATGCGA 57.534 40.909 0.00 0.00 0.00 5.10
2567 2715 9.829507 AGAAATTACTAGATCATGGACTTTCAG 57.170 33.333 0.00 0.00 0.00 3.02
2568 2716 9.605275 CAGAAATTACTAGATCATGGACTTTCA 57.395 33.333 0.00 0.00 0.00 2.69
2606 2754 3.900941 AGTGCCACAAATTGATCGAAAC 58.099 40.909 0.00 0.00 0.00 2.78
2618 2766 5.911752 ACACAAATGATAAAAGTGCCACAA 58.088 33.333 0.00 0.00 33.69 3.33
2619 2767 5.528043 ACACAAATGATAAAAGTGCCACA 57.472 34.783 0.00 0.00 33.69 4.17
2881 3029 1.432270 GCGGGTGCAGCTAAGTGATC 61.432 60.000 16.65 0.00 42.15 2.92
2926 3074 6.457528 GCCAGCTCAAGTTCATTAATACTGAC 60.458 42.308 0.00 0.00 0.00 3.51
2947 3095 2.794350 GACAACGTTCAAAATTGGCCAG 59.206 45.455 5.11 0.00 0.00 4.85
3019 3167 6.601613 CCTGGCAAGAATGTATTACCTTGTAA 59.398 38.462 10.85 0.00 38.50 2.41
3053 3201 9.311916 GTGAGGCATCTTATAATATAGCTGAAG 57.688 37.037 0.00 0.00 0.00 3.02
3199 3347 1.595993 CGAGTGAAAGCCGAGGAGGA 61.596 60.000 0.00 0.00 45.00 3.71
3264 3412 5.008217 CGAATTTGTGGACAGGTTACTCAAA 59.992 40.000 0.00 0.00 0.00 2.69
3374 3525 6.456447 TTTACACTATTGTTGTACTGCGAC 57.544 37.500 0.00 0.00 37.15 5.19
3816 3982 4.322801 CCAGTCCGAACATATAAGGGATCC 60.323 50.000 1.92 1.92 0.00 3.36
3863 4053 3.270877 GAGGGGTGTAGTTGCATACTTG 58.729 50.000 6.82 0.00 38.33 3.16
3864 4054 2.910319 TGAGGGGTGTAGTTGCATACTT 59.090 45.455 6.82 0.00 38.33 2.24
3865 4055 2.546899 TGAGGGGTGTAGTTGCATACT 58.453 47.619 6.74 6.74 41.04 2.12
3874 4064 4.651778 TCTGAACATTTTGAGGGGTGTAG 58.348 43.478 0.00 0.00 0.00 2.74
3953 4144 2.479560 GCCGGTTGTGGAATAAATGCTC 60.480 50.000 1.90 0.00 0.00 4.26
3962 4153 1.525077 GAGTGTGCCGGTTGTGGAA 60.525 57.895 1.90 0.00 0.00 3.53
3963 4154 2.110213 GAGTGTGCCGGTTGTGGA 59.890 61.111 1.90 0.00 0.00 4.02
3964 4155 3.345808 CGAGTGTGCCGGTTGTGG 61.346 66.667 1.90 0.00 0.00 4.17
4030 4242 2.565394 CGCTACGATTGACGCCGTC 61.565 63.158 10.96 10.96 46.94 4.79
4031 4243 2.578713 CGCTACGATTGACGCCGT 60.579 61.111 0.00 0.00 46.94 5.68
4032 4244 3.972803 GCGCTACGATTGACGCCG 61.973 66.667 0.00 0.00 45.35 6.46
4082 4333 2.576317 GCTACGACTGACGCCGTC 60.576 66.667 10.96 10.96 46.94 4.79
4083 4334 4.112341 GGCTACGACTGACGCCGT 62.112 66.667 0.00 0.00 46.94 5.68
4087 4338 4.156622 TCGCGGCTACGACTGACG 62.157 66.667 6.13 0.00 44.60 4.35
4088 4339 2.049475 ATCTCGCGGCTACGACTGAC 62.049 60.000 6.13 0.00 44.60 3.51
4089 4340 1.374343 AATCTCGCGGCTACGACTGA 61.374 55.000 6.13 0.00 44.60 3.41
4090 4341 0.930742 GAATCTCGCGGCTACGACTG 60.931 60.000 6.13 0.00 44.60 3.51
4091 4342 1.355916 GAATCTCGCGGCTACGACT 59.644 57.895 6.13 0.00 44.60 4.18
4092 4343 0.930742 CTGAATCTCGCGGCTACGAC 60.931 60.000 6.13 0.00 44.60 4.34
4093 4344 1.355563 CTGAATCTCGCGGCTACGA 59.644 57.895 6.13 1.86 44.60 3.43
4094 4345 1.658717 CCTGAATCTCGCGGCTACG 60.659 63.158 6.13 0.00 44.63 3.51
4095 4346 1.300233 CCCTGAATCTCGCGGCTAC 60.300 63.158 6.13 0.00 0.00 3.58
4096 4347 2.498941 CCCCTGAATCTCGCGGCTA 61.499 63.158 6.13 0.00 0.00 3.93
4097 4348 3.854669 CCCCTGAATCTCGCGGCT 61.855 66.667 6.13 0.00 0.00 5.52
4099 4350 4.161295 TGCCCCTGAATCTCGCGG 62.161 66.667 6.13 0.00 0.00 6.46
4100 4351 2.587194 CTGCCCCTGAATCTCGCG 60.587 66.667 0.00 0.00 0.00 5.87
4101 4352 2.203126 CCTGCCCCTGAATCTCGC 60.203 66.667 0.00 0.00 0.00 5.03
4102 4353 2.507944 CCCTGCCCCTGAATCTCG 59.492 66.667 0.00 0.00 0.00 4.04
4103 4354 2.194326 GCCCTGCCCCTGAATCTC 59.806 66.667 0.00 0.00 0.00 2.75
4104 4355 2.286732 AGCCCTGCCCCTGAATCT 60.287 61.111 0.00 0.00 0.00 2.40
4105 4356 2.123982 CAGCCCTGCCCCTGAATC 60.124 66.667 0.00 0.00 0.00 2.52
4133 4384 1.324383 TCGTTCAAAGGGAAAAGGCC 58.676 50.000 0.00 0.00 37.23 5.19
4134 4385 2.361119 AGTTCGTTCAAAGGGAAAAGGC 59.639 45.455 0.00 0.00 37.23 4.35
4135 4386 4.649088 AAGTTCGTTCAAAGGGAAAAGG 57.351 40.909 0.00 0.00 37.23 3.11
4136 4387 5.407502 ACAAAGTTCGTTCAAAGGGAAAAG 58.592 37.500 0.00 0.00 37.23 2.27
4137 4388 5.047943 TGACAAAGTTCGTTCAAAGGGAAAA 60.048 36.000 0.00 0.00 37.23 2.29
4138 4389 4.459685 TGACAAAGTTCGTTCAAAGGGAAA 59.540 37.500 0.00 0.00 37.23 3.13
4139 4390 4.011023 TGACAAAGTTCGTTCAAAGGGAA 58.989 39.130 0.00 0.00 0.00 3.97
4140 4391 3.375922 GTGACAAAGTTCGTTCAAAGGGA 59.624 43.478 0.00 0.00 0.00 4.20
4141 4392 3.127895 TGTGACAAAGTTCGTTCAAAGGG 59.872 43.478 0.00 0.00 0.00 3.95
4142 4393 4.349663 TGTGACAAAGTTCGTTCAAAGG 57.650 40.909 0.00 0.00 0.00 3.11
4143 4394 6.683090 TTTTGTGACAAAGTTCGTTCAAAG 57.317 33.333 10.91 0.00 0.00 2.77
4144 4395 6.863645 TCATTTTGTGACAAAGTTCGTTCAAA 59.136 30.769 10.91 0.00 0.00 2.69
4145 4396 6.382608 TCATTTTGTGACAAAGTTCGTTCAA 58.617 32.000 10.91 0.00 0.00 2.69
4146 4397 5.944013 TCATTTTGTGACAAAGTTCGTTCA 58.056 33.333 10.91 0.00 0.00 3.18
4147 4398 6.862944 TTCATTTTGTGACAAAGTTCGTTC 57.137 33.333 10.91 0.00 36.32 3.95
4148 4399 7.253618 CGAATTCATTTTGTGACAAAGTTCGTT 60.254 33.333 21.70 13.48 36.32 3.85
4149 4400 6.196353 CGAATTCATTTTGTGACAAAGTTCGT 59.804 34.615 21.70 8.26 36.32 3.85
4150 4401 6.413526 TCGAATTCATTTTGTGACAAAGTTCG 59.586 34.615 22.78 22.78 36.32 3.95
4151 4402 7.547119 GTCGAATTCATTTTGTGACAAAGTTC 58.453 34.615 10.91 10.20 36.32 3.01
4152 4403 6.196353 CGTCGAATTCATTTTGTGACAAAGTT 59.804 34.615 10.91 0.58 36.32 2.66
4153 4404 5.681105 CGTCGAATTCATTTTGTGACAAAGT 59.319 36.000 10.91 5.51 36.32 2.66
4154 4405 5.681105 ACGTCGAATTCATTTTGTGACAAAG 59.319 36.000 10.91 1.01 36.32 2.77
4155 4406 5.453909 CACGTCGAATTCATTTTGTGACAAA 59.546 36.000 6.66 6.66 36.32 2.83
4156 4407 4.966970 CACGTCGAATTCATTTTGTGACAA 59.033 37.500 6.22 0.00 36.32 3.18
4157 4408 4.271291 TCACGTCGAATTCATTTTGTGACA 59.729 37.500 6.22 0.00 36.32 3.58
4158 4409 4.768145 TCACGTCGAATTCATTTTGTGAC 58.232 39.130 6.22 2.12 36.32 3.67
4159 4410 5.411083 TTCACGTCGAATTCATTTTGTGA 57.589 34.783 6.22 8.70 33.68 3.58
4160 4411 5.681105 ACTTTCACGTCGAATTCATTTTGTG 59.319 36.000 6.22 6.61 32.32 3.33
4161 4412 5.816919 ACTTTCACGTCGAATTCATTTTGT 58.183 33.333 6.22 0.00 32.32 2.83
4162 4413 8.434870 AATACTTTCACGTCGAATTCATTTTG 57.565 30.769 6.22 0.00 32.32 2.44
4163 4414 9.113876 GAAATACTTTCACGTCGAATTCATTTT 57.886 29.630 6.22 0.00 39.45 1.82
4164 4415 8.286800 TGAAATACTTTCACGTCGAATTCATTT 58.713 29.630 6.22 0.00 44.21 2.32
4165 4416 7.802738 TGAAATACTTTCACGTCGAATTCATT 58.197 30.769 6.22 0.00 44.21 2.57
4166 4417 7.359262 TGAAATACTTTCACGTCGAATTCAT 57.641 32.000 6.22 0.00 44.21 2.57
4167 4418 6.772770 TGAAATACTTTCACGTCGAATTCA 57.227 33.333 6.22 0.00 44.21 2.57
4179 4430 7.872113 AAGGGTCAGATCATGAAATACTTTC 57.128 36.000 0.00 0.00 40.43 2.62
4180 4431 8.655935 AAAAGGGTCAGATCATGAAATACTTT 57.344 30.769 0.00 2.25 40.43 2.66
4181 4432 9.401058 CTAAAAGGGTCAGATCATGAAATACTT 57.599 33.333 0.00 0.00 40.43 2.24
4182 4433 7.500559 GCTAAAAGGGTCAGATCATGAAATACT 59.499 37.037 0.00 0.00 40.43 2.12
4183 4434 7.283127 TGCTAAAAGGGTCAGATCATGAAATAC 59.717 37.037 0.00 0.00 40.43 1.89
4184 4435 7.345691 TGCTAAAAGGGTCAGATCATGAAATA 58.654 34.615 0.00 0.00 40.43 1.40
4185 4436 6.189859 TGCTAAAAGGGTCAGATCATGAAAT 58.810 36.000 0.00 0.00 40.43 2.17
4186 4437 5.569355 TGCTAAAAGGGTCAGATCATGAAA 58.431 37.500 0.00 0.00 40.43 2.69
4187 4438 5.178096 TGCTAAAAGGGTCAGATCATGAA 57.822 39.130 0.00 0.00 40.43 2.57
4188 4439 4.842531 TGCTAAAAGGGTCAGATCATGA 57.157 40.909 0.00 0.00 34.79 3.07
4189 4440 5.735354 GCATTGCTAAAAGGGTCAGATCATG 60.735 44.000 0.16 0.00 0.00 3.07
4190 4441 4.340381 GCATTGCTAAAAGGGTCAGATCAT 59.660 41.667 0.16 0.00 0.00 2.45
4191 4442 3.696051 GCATTGCTAAAAGGGTCAGATCA 59.304 43.478 0.16 0.00 0.00 2.92
4192 4443 3.067320 GGCATTGCTAAAAGGGTCAGATC 59.933 47.826 8.82 0.00 0.00 2.75
4193 4444 3.026694 GGCATTGCTAAAAGGGTCAGAT 58.973 45.455 8.82 0.00 0.00 2.90
4194 4445 2.224992 TGGCATTGCTAAAAGGGTCAGA 60.225 45.455 8.82 0.00 0.00 3.27
4195 4446 2.094545 GTGGCATTGCTAAAAGGGTCAG 60.095 50.000 8.82 0.00 0.00 3.51
4196 4447 1.892474 GTGGCATTGCTAAAAGGGTCA 59.108 47.619 8.82 0.00 0.00 4.02
4197 4448 1.892474 TGTGGCATTGCTAAAAGGGTC 59.108 47.619 8.82 0.00 0.00 4.46
4198 4449 1.895131 CTGTGGCATTGCTAAAAGGGT 59.105 47.619 8.82 0.00 0.00 4.34
4199 4450 1.404583 GCTGTGGCATTGCTAAAAGGG 60.405 52.381 8.82 0.00 38.54 3.95
4200 4451 1.404583 GGCTGTGGCATTGCTAAAAGG 60.405 52.381 8.82 0.00 40.87 3.11
4201 4452 1.404583 GGGCTGTGGCATTGCTAAAAG 60.405 52.381 8.82 5.21 40.87 2.27
4202 4453 0.607620 GGGCTGTGGCATTGCTAAAA 59.392 50.000 8.82 0.00 40.87 1.52
4203 4454 1.594194 CGGGCTGTGGCATTGCTAAA 61.594 55.000 8.82 0.00 40.87 1.85
4204 4455 2.045708 CGGGCTGTGGCATTGCTAA 61.046 57.895 8.82 0.00 40.87 3.09
4205 4456 2.438254 CGGGCTGTGGCATTGCTA 60.438 61.111 8.82 0.00 40.87 3.49
4225 4476 1.448985 TCTATGTTGGGCAGAAACGC 58.551 50.000 0.00 0.00 0.00 4.84
4226 4477 3.821841 GTTTCTATGTTGGGCAGAAACG 58.178 45.455 9.81 0.00 44.66 3.60
4228 4479 2.227865 GCGTTTCTATGTTGGGCAGAAA 59.772 45.455 0.00 0.00 36.27 2.52
4229 4480 1.810151 GCGTTTCTATGTTGGGCAGAA 59.190 47.619 0.00 0.00 0.00 3.02
4230 4481 1.448985 GCGTTTCTATGTTGGGCAGA 58.551 50.000 0.00 0.00 0.00 4.26
4231 4482 0.451783 GGCGTTTCTATGTTGGGCAG 59.548 55.000 0.00 0.00 0.00 4.85
4232 4483 1.302383 CGGCGTTTCTATGTTGGGCA 61.302 55.000 0.00 0.00 0.00 5.36
4233 4484 1.022451 TCGGCGTTTCTATGTTGGGC 61.022 55.000 6.85 0.00 0.00 5.36
4234 4485 1.006832 CTCGGCGTTTCTATGTTGGG 58.993 55.000 6.85 0.00 0.00 4.12
4235 4486 1.006832 CCTCGGCGTTTCTATGTTGG 58.993 55.000 6.85 0.00 0.00 3.77
4236 4487 1.722011 ACCTCGGCGTTTCTATGTTG 58.278 50.000 6.85 0.00 0.00 3.33
4237 4488 2.737679 GCTACCTCGGCGTTTCTATGTT 60.738 50.000 6.85 0.00 0.00 2.71
4238 4489 1.202382 GCTACCTCGGCGTTTCTATGT 60.202 52.381 6.85 0.00 0.00 2.29
4239 4490 1.067212 AGCTACCTCGGCGTTTCTATG 59.933 52.381 6.85 0.00 34.52 2.23
4240 4491 1.400737 AGCTACCTCGGCGTTTCTAT 58.599 50.000 6.85 0.00 34.52 1.98
4241 4492 1.945394 CTAGCTACCTCGGCGTTTCTA 59.055 52.381 6.85 0.87 34.52 2.10
4242 4493 0.739561 CTAGCTACCTCGGCGTTTCT 59.260 55.000 6.85 0.00 34.52 2.52
4243 4494 0.870735 GCTAGCTACCTCGGCGTTTC 60.871 60.000 7.70 0.00 34.52 2.78
4244 4495 1.141234 GCTAGCTACCTCGGCGTTT 59.859 57.895 7.70 0.00 34.52 3.60
4245 4496 2.806237 GCTAGCTACCTCGGCGTT 59.194 61.111 7.70 0.00 34.52 4.84
4246 4497 3.584052 CGCTAGCTACCTCGGCGT 61.584 66.667 13.93 0.00 38.07 5.68
4247 4498 2.609183 AAACGCTAGCTACCTCGGCG 62.609 60.000 19.20 19.20 43.82 6.46
4248 4499 0.870735 GAAACGCTAGCTACCTCGGC 60.871 60.000 13.93 1.92 0.00 5.54
4249 4500 0.739561 AGAAACGCTAGCTACCTCGG 59.260 55.000 13.93 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.