Multiple sequence alignment - TraesCS3D01G195100

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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 TraesCS3D01G195100 chr3D 100.000 5261 0 0 1 5261 188813620 188818880 0.000000e+00 9716.0
1 TraesCS3D01G195100 chr3A 95.305 3216 65 22 60 3206 247729182 247732380 0.000000e+00 5024.0
2 TraesCS3D01G195100 chr3A 93.638 1116 38 12 3635 4730 247733133 247734235 0.000000e+00 1637.0
3 TraesCS3D01G195100 chr3A 92.617 298 8 8 3212 3497 247732458 247732753 2.930000e-112 416.0
4 TraesCS3D01G195100 chr3A 82.407 432 26 6 4595 5022 247734422 247734807 1.090000e-86 331.0
5 TraesCS3D01G195100 chr3A 92.857 140 6 2 4595 4730 247734259 247734398 3.210000e-47 200.0
6 TraesCS3D01G195100 chr3A 88.811 143 15 1 5019 5161 247737418 247737559 1.950000e-39 174.0
7 TraesCS3D01G195100 chr3B 96.730 2997 50 15 65 3028 271819400 271822381 0.000000e+00 4948.0
8 TraesCS3D01G195100 chr3B 90.886 1580 55 28 3537 5116 271823409 271824899 0.000000e+00 2037.0
9 TraesCS3D01G195100 chr3B 92.357 314 11 3 3212 3512 271822804 271823117 8.090000e-118 435.0
10 TraesCS3D01G195100 chr3B 89.691 194 5 4 3011 3189 271822560 271822753 3.170000e-57 233.0
11 TraesCS3D01G195100 chr3B 95.238 42 2 0 1 42 271819366 271819407 3.400000e-07 67.6
12 TraesCS3D01G195100 chr7D 85.294 68 9 1 3138 3204 633070939 633070872 9.450000e-08 69.4


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 TraesCS3D01G195100 chr3D 188813620 188818880 5260 False 9716.00 9716 100.000000 1 5261 1 chr3D.!!$F1 5260
1 TraesCS3D01G195100 chr3A 247729182 247737559 8377 False 1297.00 5024 90.939167 60 5161 6 chr3A.!!$F1 5101
2 TraesCS3D01G195100 chr3B 271819366 271824899 5533 False 1544.12 4948 92.980400 1 5116 5 chr3B.!!$F1 5115

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
196 201 0.827507 GGCTTGGAGGCAAACAAGGA 60.828 55.000 14.65 0.0 43.21 3.36 F
849 865 1.294780 CCGGAGAAAGCAGCTGAGT 59.705 57.895 20.43 0.0 0.00 3.41 F
1086 1102 1.748493 GACATGAGACTCTTCCTCGCT 59.252 52.381 0.00 0.0 33.51 4.93 F
2447 2520 2.375174 TCCCATATGGTATGTTCCCAGC 59.625 50.000 20.46 0.0 34.92 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1086 1102 1.610624 GCGAGTTGTTGGGAGATGGAA 60.611 52.381 0.00 0.0 0.0 3.53 R
2448 2521 0.829333 AAACACTGCATTGTTGGGCA 59.171 45.000 21.48 0.0 39.7 5.36 R
2968 3041 9.672673 GTTATCAGTATCCCAGCATAATGTATT 57.327 33.333 0.00 0.0 0.0 1.89 R
4276 4931 0.034896 GAGGAGTCACAAGGGCGAAA 59.965 55.000 0.00 0.0 0.0 3.46 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
31 32 1.146566 GCCATGAATTCTCCATCCCCT 59.853 52.381 7.05 0.00 0.00 4.79
33 34 2.715336 CCATGAATTCTCCATCCCCTCT 59.285 50.000 7.05 0.00 0.00 3.69
34 35 3.244840 CCATGAATTCTCCATCCCCTCTC 60.245 52.174 7.05 0.00 0.00 3.20
35 36 3.428063 TGAATTCTCCATCCCCTCTCT 57.572 47.619 7.05 0.00 0.00 3.10
36 37 3.312890 TGAATTCTCCATCCCCTCTCTC 58.687 50.000 7.05 0.00 0.00 3.20
37 38 3.051496 TGAATTCTCCATCCCCTCTCTCT 60.051 47.826 7.05 0.00 0.00 3.10
38 39 2.765689 TTCTCCATCCCCTCTCTCTC 57.234 55.000 0.00 0.00 0.00 3.20
39 40 1.919933 TCTCCATCCCCTCTCTCTCT 58.080 55.000 0.00 0.00 0.00 3.10
40 41 1.780309 TCTCCATCCCCTCTCTCTCTC 59.220 57.143 0.00 0.00 0.00 3.20
41 42 1.782752 CTCCATCCCCTCTCTCTCTCT 59.217 57.143 0.00 0.00 0.00 3.10
42 43 1.780309 TCCATCCCCTCTCTCTCTCTC 59.220 57.143 0.00 0.00 0.00 3.20
43 44 1.782752 CCATCCCCTCTCTCTCTCTCT 59.217 57.143 0.00 0.00 0.00 3.10
44 45 2.224867 CCATCCCCTCTCTCTCTCTCTC 60.225 59.091 0.00 0.00 0.00 3.20
45 46 2.587060 TCCCCTCTCTCTCTCTCTCT 57.413 55.000 0.00 0.00 0.00 3.10
46 47 2.408565 TCCCCTCTCTCTCTCTCTCTC 58.591 57.143 0.00 0.00 0.00 3.20
47 48 2.022035 TCCCCTCTCTCTCTCTCTCTCT 60.022 54.545 0.00 0.00 0.00 3.10
48 49 2.370189 CCCCTCTCTCTCTCTCTCTCTC 59.630 59.091 0.00 0.00 0.00 3.20
49 50 3.312890 CCCTCTCTCTCTCTCTCTCTCT 58.687 54.545 0.00 0.00 0.00 3.10
50 51 3.323403 CCCTCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.00 0.00 3.20
51 52 4.222336 CCTCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.00 0.00 3.10
52 53 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
53 54 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
54 55 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
55 56 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
56 57 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
57 58 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
58 59 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
72 73 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
74 75 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
109 110 8.160765 TGGAACACAAGAAACCTCTTATGATTA 58.839 33.333 0.41 0.00 38.18 1.75
195 200 0.829182 AGGCTTGGAGGCAAACAAGG 60.829 55.000 14.65 1.56 44.19 3.61
196 201 0.827507 GGCTTGGAGGCAAACAAGGA 60.828 55.000 14.65 0.00 43.21 3.36
267 274 5.715753 ACCCATAAATAGATACTCGTCTCCC 59.284 44.000 0.00 0.00 0.00 4.30
499 512 3.711704 CCTCTCACCTACTCTCTCTCTCT 59.288 52.174 0.00 0.00 0.00 3.10
500 513 4.202264 CCTCTCACCTACTCTCTCTCTCTC 60.202 54.167 0.00 0.00 0.00 3.20
621 634 3.823330 CTCGGTTCCCTCCCGTCG 61.823 72.222 0.00 0.00 45.63 5.12
849 865 1.294780 CCGGAGAAAGCAGCTGAGT 59.705 57.895 20.43 0.00 0.00 3.41
977 993 4.363990 AGTCGCAGTGCTCCACGG 62.364 66.667 14.33 0.00 39.64 4.94
1086 1102 1.748493 GACATGAGACTCTTCCTCGCT 59.252 52.381 0.00 0.00 33.51 4.93
1926 1979 4.687901 TGAGTTGTTCATGTTCCTCTGA 57.312 40.909 0.00 0.00 0.00 3.27
2107 2160 4.321452 CCACGCAAGGTACTAAGTTCTGTA 60.321 45.833 0.00 0.00 38.49 2.74
2132 2185 8.673626 ATGATTTTAAGCATAAACTGTGAACG 57.326 30.769 0.00 0.00 32.47 3.95
2138 2191 3.432252 AGCATAAACTGTGAACGTGCTAC 59.568 43.478 0.00 0.00 39.43 3.58
2447 2520 2.375174 TCCCATATGGTATGTTCCCAGC 59.625 50.000 20.46 0.00 34.92 4.85
2448 2521 2.376518 CCCATATGGTATGTTCCCAGCT 59.623 50.000 20.46 0.00 34.92 4.24
2697 2770 8.811994 GGTGAGAATAGCTTTAATCTCTAGGAT 58.188 37.037 14.72 0.00 39.21 3.24
2884 2957 4.223923 AGTCCGAAAATGATGACTTCCTCT 59.776 41.667 0.00 0.00 34.53 3.69
2968 3041 1.272816 TGGTTCATCGTCTCCCCACTA 60.273 52.381 0.00 0.00 0.00 2.74
3134 3403 8.662781 ATTATACACGATGTGCACTTATTCTT 57.337 30.769 19.41 0.98 36.98 2.52
3174 3473 5.699097 TTAAGATTCAACCCCAAACTTCG 57.301 39.130 0.00 0.00 0.00 3.79
3206 3505 0.115349 CCACACCCCAAATAACCCCA 59.885 55.000 0.00 0.00 0.00 4.96
3207 3506 1.483307 CCACACCCCAAATAACCCCAA 60.483 52.381 0.00 0.00 0.00 4.12
3208 3507 2.330216 CACACCCCAAATAACCCCAAA 58.670 47.619 0.00 0.00 0.00 3.28
3209 3508 2.037902 CACACCCCAAATAACCCCAAAC 59.962 50.000 0.00 0.00 0.00 2.93
3210 3509 2.090437 ACACCCCAAATAACCCCAAACT 60.090 45.455 0.00 0.00 0.00 2.66
3212 3511 2.976185 ACCCCAAATAACCCCAAACTTG 59.024 45.455 0.00 0.00 0.00 3.16
3214 3513 2.290008 CCCAAATAACCCCAAACTTGCC 60.290 50.000 0.00 0.00 0.00 4.52
3215 3514 2.370189 CCAAATAACCCCAAACTTGCCA 59.630 45.455 0.00 0.00 0.00 4.92
3216 3515 3.398406 CAAATAACCCCAAACTTGCCAC 58.602 45.455 0.00 0.00 0.00 5.01
3445 3828 9.571816 TCTGGGAAATTTTCAATAAATTTTGCT 57.428 25.926 11.09 0.00 39.23 3.91
3512 3900 5.799213 TGTCACAATTTTGACCCAGTTTTT 58.201 33.333 19.40 0.00 44.63 1.94
3513 3901 6.936279 TGTCACAATTTTGACCCAGTTTTTA 58.064 32.000 19.40 0.00 44.63 1.52
3514 3902 7.560368 TGTCACAATTTTGACCCAGTTTTTAT 58.440 30.769 19.40 0.00 44.63 1.40
3515 3903 7.708752 TGTCACAATTTTGACCCAGTTTTTATC 59.291 33.333 19.40 0.00 44.63 1.75
3516 3904 7.170828 GTCACAATTTTGACCCAGTTTTTATCC 59.829 37.037 12.80 0.00 40.15 2.59
3517 3905 6.426633 CACAATTTTGACCCAGTTTTTATCCC 59.573 38.462 0.00 0.00 0.00 3.85
3518 3906 5.755409 ATTTTGACCCAGTTTTTATCCCC 57.245 39.130 0.00 0.00 0.00 4.81
3519 3907 2.911552 TGACCCAGTTTTTATCCCCC 57.088 50.000 0.00 0.00 0.00 5.40
3533 3921 2.523168 CCCCCACACACAAACCCC 60.523 66.667 0.00 0.00 0.00 4.95
3534 3922 2.280416 CCCCACACACAAACCCCA 59.720 61.111 0.00 0.00 0.00 4.96
3535 3923 1.381872 CCCCACACACAAACCCCAA 60.382 57.895 0.00 0.00 0.00 4.12
3536 3924 0.978146 CCCCACACACAAACCCCAAA 60.978 55.000 0.00 0.00 0.00 3.28
3537 3925 0.905357 CCCACACACAAACCCCAAAA 59.095 50.000 0.00 0.00 0.00 2.44
3538 3926 1.279271 CCCACACACAAACCCCAAAAA 59.721 47.619 0.00 0.00 0.00 1.94
3585 4240 9.745018 ATCTGGACTAATCTGAGAAAATTTCAA 57.255 29.630 8.55 0.00 0.00 2.69
3642 4297 7.933728 AATTTTGAATTCTGCAATTTTTGGC 57.066 28.000 7.05 0.00 31.94 4.52
3826 4481 1.916181 ACCTAGTGGCTTAGTTGGCAT 59.084 47.619 0.00 0.00 44.18 4.40
3848 4503 1.674651 CTGCTGACATGGCACTGCT 60.675 57.895 13.44 0.00 35.71 4.24
3865 4520 3.577231 CTCAGTCAGCACTCAACGT 57.423 52.632 0.00 0.00 0.00 3.99
3997 4652 1.939934 TGCGATGGCTAGCATAAACAC 59.060 47.619 18.24 0.00 38.59 3.32
4056 4711 6.816136 TCTCTGAACATACAAACTCTTGTGA 58.184 36.000 0.81 0.00 45.53 3.58
4077 4732 6.645003 TGTGACGATATATTATTGCAGACACC 59.355 38.462 0.00 0.00 0.00 4.16
4276 4931 5.172934 TGGAATAACGTGAACTATTTCGCT 58.827 37.500 5.04 0.00 39.69 4.93
4277 4932 5.640357 TGGAATAACGTGAACTATTTCGCTT 59.360 36.000 5.04 2.08 39.69 4.68
4278 4933 6.148150 TGGAATAACGTGAACTATTTCGCTTT 59.852 34.615 5.04 4.53 39.69 3.51
4279 4934 6.681599 GGAATAACGTGAACTATTTCGCTTTC 59.318 38.462 5.04 3.53 39.69 2.62
4280 4935 3.700130 ACGTGAACTATTTCGCTTTCG 57.300 42.857 5.04 0.00 39.69 3.46
4281 4936 2.159881 ACGTGAACTATTTCGCTTTCGC 60.160 45.455 5.04 0.00 39.69 4.70
4471 5126 4.769859 TCTACGTGCAGTGTATGTAACA 57.230 40.909 13.39 2.22 35.06 2.41
4596 5267 1.325476 CCCTCCATTGCTGCTTTCCC 61.325 60.000 0.00 0.00 0.00 3.97
4689 5527 7.351952 ACTGGACACTGTAGTCACCTAATATA 58.648 38.462 10.85 0.00 40.29 0.86
4730 5731 2.026262 TCGGCTTTTCAGATAGGCCTTT 60.026 45.455 12.58 1.34 40.52 3.11
4731 5732 2.755103 CGGCTTTTCAGATAGGCCTTTT 59.245 45.455 12.58 0.00 40.52 2.27
4732 5733 3.193479 CGGCTTTTCAGATAGGCCTTTTT 59.807 43.478 12.58 0.00 40.52 1.94
4778 5788 4.286032 TGAGAGGCAAGGAAAGTAGCTTAA 59.714 41.667 0.00 0.00 0.00 1.85
4779 5789 4.580868 AGAGGCAAGGAAAGTAGCTTAAC 58.419 43.478 0.00 0.00 0.00 2.01
4780 5790 4.287326 AGAGGCAAGGAAAGTAGCTTAACT 59.713 41.667 0.00 0.00 0.00 2.24
4781 5791 5.484290 AGAGGCAAGGAAAGTAGCTTAACTA 59.516 40.000 0.00 0.00 0.00 2.24
4782 5792 5.735766 AGGCAAGGAAAGTAGCTTAACTAG 58.264 41.667 0.00 0.00 0.00 2.57
4783 5793 5.484290 AGGCAAGGAAAGTAGCTTAACTAGA 59.516 40.000 0.00 0.00 0.00 2.43
4784 5794 6.157123 AGGCAAGGAAAGTAGCTTAACTAGAT 59.843 38.462 0.00 0.00 0.00 1.98
4785 5795 6.824196 GGCAAGGAAAGTAGCTTAACTAGATT 59.176 38.462 0.00 0.00 0.00 2.40
4786 5796 7.985752 GGCAAGGAAAGTAGCTTAACTAGATTA 59.014 37.037 0.00 0.00 0.00 1.75
4829 5839 7.242359 CCTCTTTAGATCCTCCTAGATAACCA 58.758 42.308 0.00 0.00 0.00 3.67
4902 5912 4.262164 CCAAGGAAAACAATGAGGTTGAGG 60.262 45.833 0.00 0.00 40.37 3.86
4935 5945 1.350193 CTTCAATCTGTCGACCCGTG 58.650 55.000 14.12 6.21 0.00 4.94
4943 5953 2.750637 TCGACCCGTGAGAGCCTC 60.751 66.667 0.00 0.00 0.00 4.70
4971 5981 3.955471 TCCATCAACAACTTGATCCTCC 58.045 45.455 0.00 0.00 44.04 4.30
5031 8655 7.307455 GCAACTCTTTCTCTAACAAAGTGGTAG 60.307 40.741 0.00 0.00 38.98 3.18
5122 8746 0.813184 CACCATAACCTTGCTGCTGG 59.187 55.000 0.00 5.96 0.00 4.85
5165 8789 8.744568 ATTCCTTCAAGAGATTTTAGATCCAC 57.255 34.615 0.00 0.00 0.00 4.02
5166 8790 7.257790 TCCTTCAAGAGATTTTAGATCCACA 57.742 36.000 0.00 0.00 0.00 4.17
5167 8791 7.865820 TCCTTCAAGAGATTTTAGATCCACAT 58.134 34.615 0.00 0.00 0.00 3.21
5168 8792 8.992349 TCCTTCAAGAGATTTTAGATCCACATA 58.008 33.333 0.00 0.00 0.00 2.29
5169 8793 9.618890 CCTTCAAGAGATTTTAGATCCACATAA 57.381 33.333 0.00 0.00 0.00 1.90
5175 8799 9.829507 AGAGATTTTAGATCCACATAACTTCTG 57.170 33.333 0.00 0.00 0.00 3.02
5176 8800 9.606631 GAGATTTTAGATCCACATAACTTCTGT 57.393 33.333 0.00 0.00 0.00 3.41
5177 8801 9.965902 AGATTTTAGATCCACATAACTTCTGTT 57.034 29.630 0.00 0.00 39.98 3.16
5179 8803 9.965902 ATTTTAGATCCACATAACTTCTGTTCT 57.034 29.630 0.00 0.00 37.59 3.01
5180 8804 8.777865 TTTAGATCCACATAACTTCTGTTCTG 57.222 34.615 0.00 0.00 37.59 3.02
5181 8805 5.738909 AGATCCACATAACTTCTGTTCTGG 58.261 41.667 0.00 0.00 35.43 3.86
5182 8806 3.674997 TCCACATAACTTCTGTTCTGGC 58.325 45.455 0.00 0.00 35.43 4.85
5183 8807 2.416547 CCACATAACTTCTGTTCTGGCG 59.583 50.000 0.00 0.00 35.43 5.69
5184 8808 3.067106 CACATAACTTCTGTTCTGGCGT 58.933 45.455 0.00 0.00 35.43 5.68
5185 8809 3.498397 CACATAACTTCTGTTCTGGCGTT 59.502 43.478 0.00 0.00 35.43 4.84
5186 8810 3.498397 ACATAACTTCTGTTCTGGCGTTG 59.502 43.478 0.00 0.00 35.43 4.10
5187 8811 1.308998 AACTTCTGTTCTGGCGTTGG 58.691 50.000 0.00 0.00 0.00 3.77
5188 8812 1.166531 ACTTCTGTTCTGGCGTTGGC 61.167 55.000 0.00 0.00 38.90 4.52
5198 8822 2.356194 GCGTTGGCCAAGGCTTTG 60.356 61.111 41.70 20.28 45.57 2.77
5199 8823 3.128375 CGTTGGCCAAGGCTTTGT 58.872 55.556 24.08 0.00 41.60 2.83
5200 8824 1.801309 GCGTTGGCCAAGGCTTTGTA 61.801 55.000 41.70 9.89 45.57 2.41
5201 8825 0.887933 CGTTGGCCAAGGCTTTGTAT 59.112 50.000 24.08 0.00 41.60 2.29
5202 8826 1.272212 CGTTGGCCAAGGCTTTGTATT 59.728 47.619 24.08 0.00 41.60 1.89
5203 8827 2.671070 CGTTGGCCAAGGCTTTGTATTC 60.671 50.000 24.08 4.82 41.60 1.75
5204 8828 2.562738 GTTGGCCAAGGCTTTGTATTCT 59.437 45.455 21.21 0.00 41.60 2.40
5205 8829 2.170166 TGGCCAAGGCTTTGTATTCTG 58.830 47.619 0.61 0.00 41.60 3.02
5206 8830 1.134995 GGCCAAGGCTTTGTATTCTGC 60.135 52.381 11.40 2.47 41.60 4.26
5207 8831 1.821136 GCCAAGGCTTTGTATTCTGCT 59.179 47.619 7.87 0.00 38.26 4.24
5208 8832 2.232208 GCCAAGGCTTTGTATTCTGCTT 59.768 45.455 7.87 0.00 38.26 3.91
5209 8833 3.841643 CCAAGGCTTTGTATTCTGCTTG 58.158 45.455 7.87 0.00 32.21 4.01
5210 8834 3.507233 CCAAGGCTTTGTATTCTGCTTGA 59.493 43.478 7.87 0.00 32.21 3.02
5211 8835 4.479619 CAAGGCTTTGTATTCTGCTTGAC 58.520 43.478 0.00 0.00 0.00 3.18
5212 8836 4.026356 AGGCTTTGTATTCTGCTTGACT 57.974 40.909 0.00 0.00 0.00 3.41
5213 8837 4.401925 AGGCTTTGTATTCTGCTTGACTT 58.598 39.130 0.00 0.00 0.00 3.01
5214 8838 4.217118 AGGCTTTGTATTCTGCTTGACTTG 59.783 41.667 0.00 0.00 0.00 3.16
5215 8839 3.916776 GCTTTGTATTCTGCTTGACTTGC 59.083 43.478 0.00 0.00 0.00 4.01
5216 8840 4.557296 GCTTTGTATTCTGCTTGACTTGCA 60.557 41.667 0.00 0.00 38.81 4.08
5217 8841 5.512753 TTTGTATTCTGCTTGACTTGCAA 57.487 34.783 0.00 0.00 40.13 4.08
5218 8842 5.512753 TTGTATTCTGCTTGACTTGCAAA 57.487 34.783 0.00 0.00 40.13 3.68
5219 8843 5.710513 TGTATTCTGCTTGACTTGCAAAT 57.289 34.783 0.00 0.00 40.13 2.32
5220 8844 6.088016 TGTATTCTGCTTGACTTGCAAATT 57.912 33.333 0.00 0.00 40.13 1.82
5221 8845 5.921976 TGTATTCTGCTTGACTTGCAAATTG 59.078 36.000 0.00 0.00 40.13 2.32
5222 8846 4.389890 TTCTGCTTGACTTGCAAATTGT 57.610 36.364 0.00 0.00 40.13 2.71
5223 8847 4.389890 TCTGCTTGACTTGCAAATTGTT 57.610 36.364 0.00 0.00 40.13 2.83
5224 8848 4.114073 TCTGCTTGACTTGCAAATTGTTG 58.886 39.130 0.00 0.00 40.13 3.33
5248 8872 7.642071 GCTTGTTTTCTAGCATTCAATGAAA 57.358 32.000 0.00 0.00 45.30 2.69
5249 8873 8.248117 GCTTGTTTTCTAGCATTCAATGAAAT 57.752 30.769 0.00 0.00 45.30 2.17
5250 8874 9.357652 GCTTGTTTTCTAGCATTCAATGAAATA 57.642 29.630 0.00 0.00 45.30 1.40
5253 8877 9.859427 TGTTTTCTAGCATTCAATGAAATAAGG 57.141 29.630 0.00 0.00 0.00 2.69
5254 8878 9.860898 GTTTTCTAGCATTCAATGAAATAAGGT 57.139 29.630 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
33 34 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
34 35 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
35 36 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
36 37 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
37 38 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
38 39 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
39 40 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
40 41 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
41 42 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
42 43 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
43 44 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
44 45 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
45 46 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
46 47 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
47 48 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
48 49 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
49 50 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
50 51 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
51 52 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
52 53 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
53 54 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
54 55 3.005261 CCGAGAGAGAGAGAGAGAGAGAG 59.995 56.522 0.00 0.00 0.00 3.20
55 56 2.959030 CCGAGAGAGAGAGAGAGAGAGA 59.041 54.545 0.00 0.00 0.00 3.10
56 57 2.546795 GCCGAGAGAGAGAGAGAGAGAG 60.547 59.091 0.00 0.00 0.00 3.20
57 58 1.412710 GCCGAGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
58 59 1.541233 GGCCGAGAGAGAGAGAGAGAG 60.541 61.905 0.00 0.00 0.00 3.20
109 110 0.804989 GCCATGCGTTTGTTAGAGCT 59.195 50.000 0.00 0.00 0.00 4.09
195 200 0.179097 GGGCGGTTGTCATCTCTCTC 60.179 60.000 0.00 0.00 0.00 3.20
196 201 1.901085 GGGCGGTTGTCATCTCTCT 59.099 57.895 0.00 0.00 0.00 3.10
267 274 4.292178 GGATCGCAGGCGGAGGAG 62.292 72.222 14.24 0.00 40.25 3.69
499 512 5.163259 AGGGATCTTGGAAGGAGATAAGA 57.837 43.478 0.00 0.00 34.13 2.10
500 513 5.903198 AAGGGATCTTGGAAGGAGATAAG 57.097 43.478 0.00 0.00 34.13 1.73
621 634 6.981559 AGTCAAATTCGAGCTAAGATTACTCC 59.018 38.462 0.00 0.00 0.00 3.85
628 641 6.706270 AGAAACAAGTCAAATTCGAGCTAAGA 59.294 34.615 0.00 0.00 0.00 2.10
629 642 6.892691 AGAAACAAGTCAAATTCGAGCTAAG 58.107 36.000 0.00 0.00 0.00 2.18
771 787 7.953493 TCAGAAAGGGTTAGAAAAATATTGGGT 59.047 33.333 0.00 0.00 0.00 4.51
849 865 0.036164 ACAGCCGCATCAACCACTAA 59.964 50.000 0.00 0.00 0.00 2.24
977 993 0.671781 TGAGAGGCAAAGAAGCGAGC 60.672 55.000 0.00 0.00 34.64 5.03
1086 1102 1.610624 GCGAGTTGTTGGGAGATGGAA 60.611 52.381 0.00 0.00 0.00 3.53
1926 1979 6.357367 TGAAAACTAAAAGAAGACAGGAGCT 58.643 36.000 0.00 0.00 0.00 4.09
2107 2160 8.296713 ACGTTCACAGTTTATGCTTAAAATCAT 58.703 29.630 6.38 0.00 0.00 2.45
2132 2185 2.678336 GTGCCTAGAAACCATGTAGCAC 59.322 50.000 0.00 0.00 30.74 4.40
2138 2191 3.149196 AGTTGTGTGCCTAGAAACCATG 58.851 45.455 0.00 0.00 0.00 3.66
2314 2387 3.083997 GACCCGAGGTGCCCTGAT 61.084 66.667 0.00 0.00 35.25 2.90
2327 2400 1.197721 CATGTGCAAGAGTTTCGACCC 59.802 52.381 0.00 0.00 0.00 4.46
2328 2401 2.096218 GTCATGTGCAAGAGTTTCGACC 60.096 50.000 0.00 0.00 0.00 4.79
2333 2406 1.610522 GCAGGTCATGTGCAAGAGTTT 59.389 47.619 2.12 0.00 40.86 2.66
2448 2521 0.829333 AAACACTGCATTGTTGGGCA 59.171 45.000 21.48 0.00 39.70 5.36
2968 3041 9.672673 GTTATCAGTATCCCAGCATAATGTATT 57.327 33.333 0.00 0.00 0.00 1.89
3134 3403 5.124645 TCTTAAACCGAGTGGCAAGTTTAA 58.875 37.500 17.65 17.65 40.50 1.52
3174 3473 0.942252 GGTGTGGTTCGACTGGTTTC 59.058 55.000 0.00 0.00 0.00 2.78
3206 3505 0.106519 ACCTGCTGAGTGGCAAGTTT 60.107 50.000 0.00 0.00 41.94 2.66
3207 3506 0.764890 TACCTGCTGAGTGGCAAGTT 59.235 50.000 0.00 0.00 41.94 2.66
3208 3507 0.035458 GTACCTGCTGAGTGGCAAGT 59.965 55.000 0.00 0.00 41.94 3.16
3209 3508 0.035317 TGTACCTGCTGAGTGGCAAG 59.965 55.000 0.00 0.00 41.94 4.01
3210 3509 0.472044 TTGTACCTGCTGAGTGGCAA 59.528 50.000 0.00 0.00 41.94 4.52
3212 3511 0.674895 CCTTGTACCTGCTGAGTGGC 60.675 60.000 0.00 0.00 0.00 5.01
3214 3513 2.839486 TTCCTTGTACCTGCTGAGTG 57.161 50.000 0.00 0.00 0.00 3.51
3215 3514 2.616510 GCATTCCTTGTACCTGCTGAGT 60.617 50.000 0.00 0.00 0.00 3.41
3216 3515 2.012673 GCATTCCTTGTACCTGCTGAG 58.987 52.381 0.00 0.00 0.00 3.35
3516 3904 2.523168 GGGGTTTGTGTGTGGGGG 60.523 66.667 0.00 0.00 0.00 5.40
3517 3905 0.978146 TTTGGGGTTTGTGTGTGGGG 60.978 55.000 0.00 0.00 0.00 4.96
3518 3906 0.905357 TTTTGGGGTTTGTGTGTGGG 59.095 50.000 0.00 0.00 0.00 4.61
3519 3907 2.770164 TTTTTGGGGTTTGTGTGTGG 57.230 45.000 0.00 0.00 0.00 4.17
3536 3924 9.768662 AGATGCTATGTTTGATTTTCAGTTTTT 57.231 25.926 0.00 0.00 0.00 1.94
3537 3925 9.199982 CAGATGCTATGTTTGATTTTCAGTTTT 57.800 29.630 0.00 0.00 0.00 2.43
3538 3926 7.816031 CCAGATGCTATGTTTGATTTTCAGTTT 59.184 33.333 0.00 0.00 0.00 2.66
3539 3927 7.177216 TCCAGATGCTATGTTTGATTTTCAGTT 59.823 33.333 0.00 0.00 0.00 3.16
3540 3928 6.660521 TCCAGATGCTATGTTTGATTTTCAGT 59.339 34.615 0.00 0.00 0.00 3.41
3585 4240 7.327975 TCTACCAATCTGTTCGACAAATATGT 58.672 34.615 0.00 0.00 44.25 2.29
3686 4341 1.951602 TCCACATGCTATGCTTGATGC 59.048 47.619 11.46 0.00 37.20 3.91
3848 4503 3.272766 CACGTTGAGTGCTGACTGA 57.727 52.632 0.00 0.00 44.72 3.41
3865 4520 3.278574 CTCACTGAAGTGGTTTTGACCA 58.721 45.455 10.45 0.00 45.65 4.02
3984 4639 5.399013 ACCAATTTTCGTGTTTATGCTAGC 58.601 37.500 8.10 8.10 0.00 3.42
3997 4652 5.988092 TCCGTTTAACAGTACCAATTTTCG 58.012 37.500 0.00 0.00 0.00 3.46
4056 4711 5.633601 CACGGTGTCTGCAATAATATATCGT 59.366 40.000 0.00 0.00 0.00 3.73
4077 4732 0.798776 GATTGAACTCCAGCACCACG 59.201 55.000 0.00 0.00 0.00 4.94
4276 4931 0.034896 GAGGAGTCACAAGGGCGAAA 59.965 55.000 0.00 0.00 0.00 3.46
4277 4932 1.671742 GAGGAGTCACAAGGGCGAA 59.328 57.895 0.00 0.00 0.00 4.70
4278 4933 2.283529 GGAGGAGTCACAAGGGCGA 61.284 63.158 0.00 0.00 0.00 5.54
4279 4934 2.266055 GGAGGAGTCACAAGGGCG 59.734 66.667 0.00 0.00 0.00 6.13
4280 4935 2.671682 GGGAGGAGTCACAAGGGC 59.328 66.667 0.00 0.00 0.00 5.19
4281 4936 1.229658 AGGGGAGGAGTCACAAGGG 60.230 63.158 0.00 0.00 0.00 3.95
4535 5190 7.664318 ACCTGTCCGTAAATCTGAACTAAATTT 59.336 33.333 0.00 0.00 0.00 1.82
4570 5225 1.746516 GCAGCAATGGAGGGAGAGAAG 60.747 57.143 0.00 0.00 0.00 2.85
4596 5267 4.156008 GTGTTTTACTTGCTACCTGATGGG 59.844 45.833 0.00 0.00 41.89 4.00
4734 5735 9.965824 CTCTCAAATCTTTTGCCTAGTTTTAAA 57.034 29.630 0.00 0.00 0.00 1.52
4735 5736 8.576442 CCTCTCAAATCTTTTGCCTAGTTTTAA 58.424 33.333 0.00 0.00 0.00 1.52
4736 5737 7.309194 GCCTCTCAAATCTTTTGCCTAGTTTTA 60.309 37.037 0.00 0.00 0.00 1.52
4737 5738 6.517362 GCCTCTCAAATCTTTTGCCTAGTTTT 60.517 38.462 0.00 0.00 0.00 2.43
4738 5739 5.047731 GCCTCTCAAATCTTTTGCCTAGTTT 60.048 40.000 0.00 0.00 0.00 2.66
4739 5740 4.460731 GCCTCTCAAATCTTTTGCCTAGTT 59.539 41.667 0.00 0.00 0.00 2.24
4740 5741 4.013050 GCCTCTCAAATCTTTTGCCTAGT 58.987 43.478 0.00 0.00 0.00 2.57
4741 5742 4.012374 TGCCTCTCAAATCTTTTGCCTAG 58.988 43.478 0.00 0.00 0.00 3.02
4742 5743 4.032960 TGCCTCTCAAATCTTTTGCCTA 57.967 40.909 0.00 0.00 0.00 3.93
4743 5744 2.880443 TGCCTCTCAAATCTTTTGCCT 58.120 42.857 0.00 0.00 0.00 4.75
4744 5745 3.582780 CTTGCCTCTCAAATCTTTTGCC 58.417 45.455 0.00 0.00 33.65 4.52
4745 5746 3.256631 TCCTTGCCTCTCAAATCTTTTGC 59.743 43.478 0.00 0.00 33.65 3.68
4746 5747 5.458041 TTCCTTGCCTCTCAAATCTTTTG 57.542 39.130 0.00 0.00 33.65 2.44
4747 5748 5.600069 ACTTTCCTTGCCTCTCAAATCTTTT 59.400 36.000 0.00 0.00 33.65 2.27
4748 5749 5.143369 ACTTTCCTTGCCTCTCAAATCTTT 58.857 37.500 0.00 0.00 33.65 2.52
4749 5750 4.734266 ACTTTCCTTGCCTCTCAAATCTT 58.266 39.130 0.00 0.00 33.65 2.40
4750 5751 4.379302 ACTTTCCTTGCCTCTCAAATCT 57.621 40.909 0.00 0.00 33.65 2.40
4751 5752 4.095632 GCTACTTTCCTTGCCTCTCAAATC 59.904 45.833 0.00 0.00 33.65 2.17
4752 5753 4.013050 GCTACTTTCCTTGCCTCTCAAAT 58.987 43.478 0.00 0.00 33.65 2.32
4753 5754 3.073062 AGCTACTTTCCTTGCCTCTCAAA 59.927 43.478 0.00 0.00 33.65 2.69
4754 5755 2.639839 AGCTACTTTCCTTGCCTCTCAA 59.360 45.455 0.00 0.00 0.00 3.02
4755 5756 2.260822 AGCTACTTTCCTTGCCTCTCA 58.739 47.619 0.00 0.00 0.00 3.27
4782 5792 9.189156 AGAGGCATTAGAGATAGAGATGTAATC 57.811 37.037 0.00 0.00 46.04 1.75
4783 5793 9.545928 AAGAGGCATTAGAGATAGAGATGTAAT 57.454 33.333 0.00 0.00 0.00 1.89
4784 5794 8.948401 AAGAGGCATTAGAGATAGAGATGTAA 57.052 34.615 0.00 0.00 0.00 2.41
4785 5795 8.948401 AAAGAGGCATTAGAGATAGAGATGTA 57.052 34.615 0.00 0.00 0.00 2.29
4786 5796 7.854166 AAAGAGGCATTAGAGATAGAGATGT 57.146 36.000 0.00 0.00 0.00 3.06
4829 5839 8.567948 CCTGATTGTAACAAACTTGTATTCTGT 58.432 33.333 0.00 0.00 41.31 3.41
4870 5880 7.353414 TCATTGTTTTCCTTGGTTGTGATAA 57.647 32.000 0.00 0.00 0.00 1.75
4935 5945 2.365617 TGATGGATTTACCGAGGCTCTC 59.634 50.000 13.50 1.64 42.61 3.20
4943 5953 5.621197 TCAAGTTGTTGATGGATTTACCG 57.379 39.130 2.11 0.00 37.79 4.02
4971 5981 7.715265 ACTTGACATTATACTTATTCCTGCG 57.285 36.000 0.00 0.00 0.00 5.18
5003 6013 6.425504 CACTTTGTTAGAGAAAGAGTTGCAG 58.574 40.000 4.80 0.00 34.94 4.41
5051 8675 4.686191 ATCCTGTGTTTCATGCCAAAAA 57.314 36.364 0.00 0.00 0.00 1.94
5154 8778 9.219603 CAGAACAGAAGTTATGTGGATCTAAAA 57.780 33.333 3.46 0.00 40.98 1.52
5161 8785 3.674997 GCCAGAACAGAAGTTATGTGGA 58.325 45.455 3.46 0.00 43.60 4.02
5162 8786 2.416547 CGCCAGAACAGAAGTTATGTGG 59.583 50.000 3.46 2.68 43.60 4.17
5163 8787 3.067106 ACGCCAGAACAGAAGTTATGTG 58.933 45.455 3.46 0.00 43.60 3.21
5164 8788 3.402628 ACGCCAGAACAGAAGTTATGT 57.597 42.857 0.00 0.00 43.60 2.29
5165 8789 3.120199 CCAACGCCAGAACAGAAGTTATG 60.120 47.826 0.00 0.00 44.45 1.90
5166 8790 3.074412 CCAACGCCAGAACAGAAGTTAT 58.926 45.455 0.00 0.00 38.30 1.89
5167 8791 2.489971 CCAACGCCAGAACAGAAGTTA 58.510 47.619 0.00 0.00 38.30 2.24
5168 8792 1.308998 CCAACGCCAGAACAGAAGTT 58.691 50.000 0.00 0.00 41.64 2.66
5169 8793 1.166531 GCCAACGCCAGAACAGAAGT 61.167 55.000 0.00 0.00 0.00 3.01
5170 8794 1.576421 GCCAACGCCAGAACAGAAG 59.424 57.895 0.00 0.00 0.00 2.85
5171 8795 3.744559 GCCAACGCCAGAACAGAA 58.255 55.556 0.00 0.00 0.00 3.02
5181 8805 1.801309 TACAAAGCCTTGGCCAACGC 61.801 55.000 26.39 26.39 36.82 4.84
5182 8806 0.887933 ATACAAAGCCTTGGCCAACG 59.112 50.000 16.05 12.50 36.82 4.10
5183 8807 2.562738 AGAATACAAAGCCTTGGCCAAC 59.437 45.455 16.05 5.95 36.82 3.77
5184 8808 2.562298 CAGAATACAAAGCCTTGGCCAA 59.438 45.455 19.25 19.25 36.82 4.52
5185 8809 2.170166 CAGAATACAAAGCCTTGGCCA 58.830 47.619 0.00 0.00 36.82 5.36
5186 8810 1.134995 GCAGAATACAAAGCCTTGGCC 60.135 52.381 8.17 0.00 36.82 5.36
5187 8811 1.821136 AGCAGAATACAAAGCCTTGGC 59.179 47.619 2.97 2.97 36.82 4.52
5188 8812 3.507233 TCAAGCAGAATACAAAGCCTTGG 59.493 43.478 0.00 0.00 36.82 3.61
5189 8813 4.217118 AGTCAAGCAGAATACAAAGCCTTG 59.783 41.667 0.00 0.00 38.61 3.61
5190 8814 4.401925 AGTCAAGCAGAATACAAAGCCTT 58.598 39.130 0.00 0.00 0.00 4.35
5191 8815 4.026356 AGTCAAGCAGAATACAAAGCCT 57.974 40.909 0.00 0.00 0.00 4.58
5192 8816 4.479619 CAAGTCAAGCAGAATACAAAGCC 58.520 43.478 0.00 0.00 0.00 4.35
5193 8817 3.916776 GCAAGTCAAGCAGAATACAAAGC 59.083 43.478 0.00 0.00 0.00 3.51
5194 8818 5.112220 TGCAAGTCAAGCAGAATACAAAG 57.888 39.130 0.00 0.00 37.02 2.77
5195 8819 5.512753 TTGCAAGTCAAGCAGAATACAAA 57.487 34.783 0.00 0.00 43.75 2.83
5196 8820 5.512753 TTTGCAAGTCAAGCAGAATACAA 57.487 34.783 0.00 0.00 43.75 2.41
5197 8821 5.710513 ATTTGCAAGTCAAGCAGAATACA 57.289 34.783 0.00 0.00 43.75 2.29
5198 8822 5.922544 ACAATTTGCAAGTCAAGCAGAATAC 59.077 36.000 0.00 0.00 43.75 1.89
5199 8823 6.088016 ACAATTTGCAAGTCAAGCAGAATA 57.912 33.333 0.00 0.00 43.75 1.75
5200 8824 4.952460 ACAATTTGCAAGTCAAGCAGAAT 58.048 34.783 0.00 0.00 43.75 2.40
5201 8825 4.389890 ACAATTTGCAAGTCAAGCAGAA 57.610 36.364 0.00 0.00 43.75 3.02
5202 8826 4.114073 CAACAATTTGCAAGTCAAGCAGA 58.886 39.130 0.00 0.00 43.75 4.26
5203 8827 4.446857 CAACAATTTGCAAGTCAAGCAG 57.553 40.909 0.00 0.00 43.75 4.24
5215 8839 6.586868 TGCTAGAAAACAAGCAACAATTTG 57.413 33.333 0.00 0.00 45.36 2.32
5224 8848 7.642071 TTTCATTGAATGCTAGAAAACAAGC 57.358 32.000 0.00 0.00 39.25 4.01
5227 8851 9.859427 CCTTATTTCATTGAATGCTAGAAAACA 57.141 29.630 0.00 0.00 32.65 2.83
5228 8852 9.860898 ACCTTATTTCATTGAATGCTAGAAAAC 57.139 29.630 0.00 0.00 32.65 2.43


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

AutoCloner maintained by Alex Coulton.