Locus 1371

Sequence ID	X_DroMel_CAF1
Location	4,106,935 – 4,107,169
Length	234
Max. P	0.999847

overview

Window 1

Location	4,106,935 – 4,107,035
Length	100
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	73.97
Mean single sequence MFE	-30.84
Consensus MFE	-19.92
Energy contribution	-20.84
Covariance contribution	0.92
Combinations/Pair	1.23
Mean z-score	-1.36
Structure conservation index	0.65
SVM decision value	0.00
SVM RNA-class probability	0.535979
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4106935 100 - 22224390
AAUUGCAAGCGGUGCACAAAACCACUAC---CCA--------AUCGCCCAAUCGCCCAACCGCCCACCGAUCGGCGACGUG----CGGGGGCGUGGCACGUCAGCG-CCACC----AAAA
.((((..((.(((.......))).))..---.))--------)).((((...(((.(...((((........))))..).)----)).))))(((((.(....).)-)))).----.... ( -31.40)
>DroSec_CAF1 118740 103 - 1
AAUUGCAAGCGGUGCACAAAAGCAUUACCCCCCA--------AUCGAACAACCGCCCAACCGCCCACCGAUCGGCGACGUG----CGGGGGCGUGGCACGUCAGCG-CCACC----AAAA
........(((((((......)).........(.--------...)....)))))......((((.(((..((....))..----)))))))(((((.(....).)-)))).----.... ( -32.80)
>DroSim_CAF1 119909 112 - 1
AAUUGCAAGCGGUGCACAAAAGCAUUACCCCCCAAUCGCCCAAUCGAACAACCGCCCAACCGCCCACCGAUCGGCGACGUG----CGGGGGCGUGGCACGUCAGCGACCGCC----AAAA
........(((((((....................(((......)))......(((....(((((.(((..((....))..----)))))))).)))......)).))))).----.... ( -34.60)
>DroEre_CAF1 125090 84 - 1
AAUUGCAAGCGGUGCACAAAAGCACUACC---------------------------CAACCGCCCACCAAUCGGCGACGUG----CGGGGGCGUGGCACGUCAGCG-CCACC----AAAA
..........(((((......)))))...---------------------------.....((((.((...((....))..----.))))))(((((.(....).)-)))).----.... ( -29.70)
>DroAna_CAF1 148245 107 - 1
AGUUGCAAGCGCUGCACAA-AGCACCAC---UCU--------AACACACAACCACCUCCACAUCCGCCUCUCGUGUGUAUGUUAAAGGGGGCGUGGCAUGUCAGCA-CCACCACCGAAAA
.((((((.(((((......-))).....---...--------....(((..((.(((..((((.((((....).))).))))...)))))..))))).)).)))).-............. ( -25.70)
>consensus
AAUUGCAAGCGGUGCACAAAAGCACUACC__CCA________AUCGAACAACCGCCCAACCGCCCACCGAUCGGCGACGUG____CGGGGGCGUGGCACGUCAGCG_CCACC____AAAA
....((..(((((((......))))............................(((....(((((.(((..((....))......)))))))).))).)))..))............... (-19.92 = -20.84 +   0.92)

alignment

secondary structure

dotplot

Window 2

Location	4,106,966 – 4,107,075
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.51
Mean single sequence MFE	-22.15
Consensus MFE	-14.63
Energy contribution	-15.05
Covariance contribution	0.42
Combinations/Pair	1.24
Mean z-score	-1.97
Structure conservation index	0.66
SVM decision value	1.31
SVM RNA-class probability	0.940801
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4106966 109 - 22224390
UAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGCGCACAAAAUUGCAAGCGGUGCACAAAACCACUAC---CCA--------AUCGCCCAAUCGCCCAACCGCCCACCGAUCGGCGACGU
...........((((.......))))....(((((((......))).((.(((.......))).))..---...--------...))))..(((((....((.....))...)))))... ( -24.90)
>DroSec_CAF1 118771 112 - 1
UAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGAGCACAAAAUUGCAAGCGGUGCACAAAAGCAUUACCCCCCA--------AUCGAACAACCGCCCAACCGCCCACCGAUCGGCGACGU
..((.......((((.......))))....(((.(((......)))..(..((((......))))..)..))).--------...)).............((((........)))).... ( -21.30)
>DroSim_CAF1 119941 120 - 1
UAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGCGCACAAAAUUGCAAGCGGUGCACAAAAGCAUUACCCCCCAAUCGCCCAAUCGAACAACCGCCCAACCGCCCACCGAUCGGCGACGU
.(((.......((((.......))))....(((((((......)))..(((((((......))............(((......)))...)))))......))))...)))((....)). ( -26.30)
>DroEre_CAF1 125121 93 - 1
UAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGCGCUCAAAAUUGCAAGCGGUGCACAAAAGCACUACC---------------------------CAACCGCCCACCAAUCGGCGACGU
...........((((.......))))....((((((........))....(((((......)))))...---------------------------.....))))......((....)). ( -21.60)
>DroYak_CAF1 118415 92 - 1
UAUCUAAUUAAGCAAAACAAAAUUGCAUUAGGGCGCACAAAAUUGCAAGCGGUGCACAAAAGCACUACC---------------------------CAA-CGCCCACCACCCGGCGACGU
...........((((.......))))....(((((((......)))....(((((......)))))...---------------------------...-.))))......((....)). ( -22.30)
>DroAna_CAF1 148284 106 - 1
UAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGCGA--AAAGUUGCAAGCGCUGCACAA-AGCACCAC---UCU--------AACACACAACCACCUCCACAUCCGCCUCUCGUGUGUAU
...........((((.......))))....((((((--....))))....(((......-))).))..---...--------.((((((.......................)))))).. ( -16.50)
>consensus
UAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGCGCACAAAAUUGCAAGCGGUGCACAAAAGCACUACC__CCA________AUCG_ACAACCGCCCAACCGCCCACCGAUCGGCGACGU
...........((((.......))))....((((((........))....(((((......)))))...................................))))......((....)). (-14.63 = -15.05 +   0.42)

alignment

secondary structure

dotplot

Window 3

Location	4,107,035 – 4,107,155
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.33
Mean single sequence MFE	-39.18
Consensus MFE	-36.14
Energy contribution	-36.78
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-3.19
Structure conservation index	0.92
SVM decision value	4.24
SVM RNA-class probability	0.999847
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4107035 120 + 22224390
UUGUGCGCCCUAAUGCAAUUUUGUUUUGCUUAAUUUGAUAGGCGUUGUCAGCUGAGCUGCCAGCCUGACAAUGUGUCCACCUAACAGGAGCAACAAUGGCAAAAUUGCACACCAGCAACA
.(((..((.....((((((((((((((((((...(((.((((((((((((((((......))).)))))))))......)))).)))))))))....)))))))))))).....)).))) ( -39.60)
>DroSec_CAF1 118843 120 + 1
UUGUGCUCCCUAAUGCAAUUUUGUUUUGCUUAAUUUGAUAGGCGUUGUCAGCUGAGCUGCCAGCCUGACAAUGUGUCCACCUAACAGGAGCAACAAUGGCAAAAUUGCACACCAGCAACA
...((((......((((((((((((((((((...(((.((((((((((((((((......))).)))))))))......)))).)))))))))....))))))))))))....))))... ( -40.00)
>DroSim_CAF1 120021 120 + 1
UUGUGCGCCCUAAUGCAAUUUUGUUUUGCUUAAUUUGAUAGGCGUUGUCAGCUGAGCUGCCAGCCUGACAAUGUGUCCACCUAACAGGAGCAACAAUGGCAAAAUUGCACACCAGCAACA
.(((..((.....((((((((((((((((((...(((.((((((((((((((((......))).)))))))))......)))).)))))))))....)))))))))))).....)).))) ( -39.60)
>DroEre_CAF1 125174 120 + 1
UUGAGCGCCCUAAUGCAAUUUUGUUUUGCUUAAUUUGAUAGGCGUUGUCAGCUGAGCUGCCAGCCUGACAAUGUGUCCACCUAACAGGAGCAACAAUGGCAAAAUUGCAAACCAGCAACA
......((.....((((((((((((((((((...(((.((((((((((((((((......))).)))))))))......)))).)))))))))....)))))))))))).....)).... ( -39.00)
>DroYak_CAF1 118467 120 + 1
UUGUGCGCCCUAAUGCAAUUUUGUUUUGCUUAAUUAGAUAGGCGUUGUCAGCGGAGCUGCCAGCCUGACAAUGUGUCUACCUAACAGGAGCAACAAUAGCAAAAUGGCACACCAGCAACA
.(((((((......)).((((((((((((((..((((.((((((((((((((((.....)).).))))))))..))))).))))...))))))....)))))))).)))))......... ( -37.70)
>consensus
UUGUGCGCCCUAAUGCAAUUUUGUUUUGCUUAAUUUGAUAGGCGUUGUCAGCUGAGCUGCCAGCCUGACAAUGUGUCCACCUAACAGGAGCAACAAUGGCAAAAUUGCACACCAGCAACA
...(((.......((((((((((((((((((....((.((((((((((((((((......))).)))))))))......)))).)).))))))....)))))))))))).....)))... (-36.14 = -36.78 +   0.64)

alignment

secondary structure

dotplot

Window 4

Location	4,107,035 – 4,107,155
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.33
Mean single sequence MFE	-40.22
Consensus MFE	-35.24
Energy contribution	-36.64
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-2.86
Structure conservation index	0.88
SVM decision value	3.16
SVM RNA-class probability	0.998608
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4107035 120 - 22224390
UGUUGCUGGUGUGCAAUUUUGCCAUUGUUGCUCCUGUUAGGUGGACACAUUGUCAGGCUGGCAGCUCAGCUGACAACGCCUAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGCGCACAA
(((((((...(((((((((((...(((((.....((.((((((......(((((((.((((....))))))))))))))))).)).....)))))..)))))))))))...)))).))). ( -40.90)
>DroSec_CAF1 118843 120 - 1
UGUUGCUGGUGUGCAAUUUUGCCAUUGUUGCUCCUGUUAGGUGGACACAUUGUCAGGCUGGCAGCUCAGCUGACAACGCCUAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGAGCACAA
((((.((...(((((((((((...(((((.....((.((((((......(((((((.((((....))))))))))))))))).)).....)))))..)))))))))))..)).))))... ( -41.00)
>DroSim_CAF1 120021 120 - 1
UGUUGCUGGUGUGCAAUUUUGCCAUUGUUGCUCCUGUUAGGUGGACACAUUGUCAGGCUGGCAGCUCAGCUGACAACGCCUAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGCGCACAA
(((((((...(((((((((((...(((((.....((.((((((......(((((((.((((....))))))))))))))))).)).....)))))..)))))))))))...)))).))). ( -40.90)
>DroEre_CAF1 125174 120 - 1
UGUUGCUGGUUUGCAAUUUUGCCAUUGUUGCUCCUGUUAGGUGGACACAUUGUCAGGCUGGCAGCUCAGCUGACAACGCCUAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGCGCUCAA
....(((....((((((((((...(((((.....((.((((((......(((((((.((((....))))))))))))))))).)).....)))))..))))))))))....)))...... ( -37.40)
>DroYak_CAF1 118467 120 - 1
UGUUGCUGGUGUGCCAUUUUGCUAUUGUUGCUCCUGUUAGGUAGACACAUUGUCAGGCUGGCAGCUCCGCUGACAACGCCUAUCUAAUUAAGCAAAACAAAAUUGCAUUAGGGCGCACAA
........(((((((....(((.(((.(((((...(((((((((((.....))).(((((.((((...)))).))..)))))))))))..))))).....))).)))....))))))).. ( -40.90)
>consensus
UGUUGCUGGUGUGCAAUUUUGCCAUUGUUGCUCCUGUUAGGUGGACACAUUGUCAGGCUGGCAGCUCAGCUGACAACGCCUAUCAAAUUAAGCAAAACAAAAUUGCAUUAGGGCGCACAA
(((((((...(((((((((((...(((((.....((.((((((......(((((((.((((....))))))))))))))))).)).....)))))..)))))))))))...)))).))). (-35.24 = -36.64 +   1.40)

alignment

secondary structure

dotplot

Window 5

Location	4,107,075 – 4,107,169
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	96.17
Mean single sequence MFE	-29.40
Consensus MFE	-25.82
Energy contribution	-26.46
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.28
Structure conservation index	0.88
SVM decision value	2.72
SVM RNA-class probability	0.996631
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4107075 94 + 22224390
GGCGUUGUCAGCUGAGCUGCCAGCCUGACAAUGUGUCCACCUAACAGGAGCAACAAUGGCAAAAUUGCACACCAGCAACAUGCAACAUGGUGCA
.(((((((((((((......))).)))))))))).(((........)))(((...((((((...((((......))))..)))..)))..))). ( -30.30)
>DroSec_CAF1 118883 94 + 1
GGCGUUGUCAGCUGAGCUGCCAGCCUGACAAUGUGUCCACCUAACAGGAGCAACAAUGGCAAAAUUGCACACCAGCAACAAGAAACAUGGUGCA
.(((((((((((((......))).)))))))))).(((........)))(((...(((......((((......)))).......)))..))). ( -28.42)
>DroSim_CAF1 120061 94 + 1
GGCGUUGUCAGCUGAGCUGCCAGCCUGACAAUGUGUCCACCUAACAGGAGCAACAAUGGCAAAAUUGCACACCAGCAACAUGCAACAUGGUGCA
.(((((((((((((......))).)))))))))).(((........)))(((...((((((...((((......))))..)))..)))..))). ( -30.30)
>DroEre_CAF1 125214 94 + 1
GGCGUUGUCAGCUGAGCUGCCAGCCUGACAAUGUGUCCACCUAACAGGAGCAACAAUGGCAAAAUUGCAAACCAGCAACAUGCAACUUGGUGCA
.(((((((((((((......))).)))))))))).(((........)))(((.(((..(((...((((......))))..)))...))).))). ( -31.40)
>DroYak_CAF1 118507 94 + 1
GGCGUUGUCAGCGGAGCUGCCAGCCUGACAAUGUGUCUACCUAACAGGAGCAACAAUAGCAAAAUGGCACACCAGCAACAUGCAACAUGAUGCA
((.(((((((((((.....)).).))))))))(((((..((.....)).((.......)).....))))).)).(((.((((...)))).))). ( -26.60)
>consensus
GGCGUUGUCAGCUGAGCUGCCAGCCUGACAAUGUGUCCACCUAACAGGAGCAACAAUGGCAAAAUUGCACACCAGCAACAUGCAACAUGGUGCA
.(((((((((((((......))).)))))))))).(((........)))(((.((...(((...((((......))))..)))....)).))). (-25.82 = -26.46 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:38 2006