Locus 4294

Sequence ID	3L_DroMel_CAF1
Location	12,604,108 – 12,604,243
Length	135
Max. P	0.898378

overview

Window 3

Location	12,604,108 – 12,604,203
Length	95
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	86.48
Mean single sequence MFE	-17.44
Consensus MFE	-14.21
Energy contribution	-14.53
Covariance contribution	0.32
Combinations/Pair	1.19
Mean z-score	-1.93
Structure conservation index	0.81
SVM decision value	1.00
SVM RNA-class probability	0.898378
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12604108 95 + 23771897
UAAAGAAUUU-UUUCAUAAAUCUCCGCAUUUGCAUUAUUUUCGACUCAAGCAAUAUAUAGUAAUUAGAGUCGAAAAAGGCGAACAUGCAACAAUUA
....(((...-.)))..........((((((((....((((((((((...................))))))))))..))))..))))........ ( -19.91)
>DroSec_CAF1 91984 93 + 1
UAAAGAAUUUUUUUCAUGAAUCUCCGCAUUUGCAUUAUUUUUGACUCGAGAAGUAUA---UAAUUAGAGUCGAAAAAGGCGAACAUGCAACAAUUA
....(((.....)))..........((((((((....((((((((((...((.....---...)).))))))))))..))))..))))........ ( -18.70)
>DroSim_CAF1 94793 91 + 1
UAAAGAAUUUUUUUCAUGAAUCUCCGCAUUUGCAUUAUUUUCGACUCGAGAA--AUA---UAAUUAGAGUCGAAAAAGGCGAACAUGCAACAAUUA
....(((.....)))..........((((((((....((((((((((.....--...---......))))))))))..))))..))))........ ( -20.94)
>DroEre_CAF1 95247 87 + 1
UGAAGAAUUC--UUCAUGAAUCUCCGUAUUUGCAUUAUUUUCGACUUAAGCA--AUA---UAAUUAAAGCCAAA--AGGCGAACAUGCAACUUCUA
.((((.((((--.....))))........((((((....((((.(((..((.--...---........))...)--)).)))).)))))))))).. ( -12.90)
>DroYak_CAF1 95644 89 + 1
UAAAGAAUUU--UUCAUGAAUCUCCGCAUUUGCAUUAUUUUCGACUUAAGCA--AUA---UAAUUAAAGUCAAAAUAGGCAAGCAUGCAACAUCUA
..........--.............((((((((.(((((((.(((((.....--...---......))))))))))))))))..))))........ ( -14.74)
>consensus
UAAAGAAUUU_UUUCAUGAAUCUCCGCAUUUGCAUUAUUUUCGACUCAAGCA__AUA___UAAUUAGAGUCGAAAAAGGCGAACAUGCAACAAUUA
....(((.....)))..........((((((((....((((((((((...................))))))))))..))))..))))........ (-14.21 = -14.53 +   0.32)

alignment

secondary structure

dotplot

Window 4

Location	12,604,129 – 12,604,243
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	86.65
Mean single sequence MFE	-17.70
Consensus MFE	-14.95
Energy contribution	-15.27
Covariance contribution	0.32
Combinations/Pair	1.20
Mean z-score	-1.49
Structure conservation index	0.84
SVM decision value	0.18
SVM RNA-class probability	0.622694
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12604129 114 + 23771897
UCCGCAUUUGCAUUAUUUUCGACUCAAGCAAUAUAUAGUAAUUAGAGUCGAAAAAGGCGAACAUGCAACAAUUAUAUUUAAAUCAUCUCACUCUUUUCCGCUAAAACCAUGCAU
...((((((((....((((((((((...................))))))))))..))))..)))).................................((.........)).. ( -20.21)
>DroSec_CAF1 92006 111 + 1
UCCGCAUUUGCAUUAUUUUUGACUCGAGAAGUAUA---UAAUUAGAGUCGAAAAAGGCGAACAUGCAACAAUUAUAUUUAAAUCAUCGCACUCUUUUCCGCUAAAACCAUGCAU
...((((((((....((((((((((...((.....---...)).))))))))))..))))..)))).....................(((...((((.....))))...))).. ( -19.20)
>DroSim_CAF1 94815 109 + 1
UCCGCAUUUGCAUUAUUUUCGACUCGAGAA--AUA---UAAUUAGAGUCGAAAAAGGCGAACAUGCAACAAUUAUAUUUAAAUCUACUCACUCUUUUCCGCUAAAACCAUGCAU
...((((((((....((((((((((.....--...---......))))))))))..))))..)))).................................((.........)).. ( -21.24)
>DroEre_CAF1 95267 107 + 1
UCCGUAUUUGCAUUAUUUUCGACUUAAGCA--AUA---UAAUUAAAGCCAAA--AGGCGAACAUGCAACUUCUAUAUUUAAAUCGCCUCACUCAAUUCCGCUUAAACCAUGCAU
........(((((.......(..((((((.--...---........(((...--.)))(((........)))...........................))))))..)))))). ( -12.11)
>DroYak_CAF1 95664 109 + 1
UCCGCAUUUGCAUUAUUUUCGACUUAAGCA--AUA---UAAUUAAAGUCAAAAUAGGCAAGCAUGCAACAUCUAUAUUUAAAUAAACUCACUCUAUUCCGCUUAAGCCAUGCAA
...((((((((.(((((((.(((((.....--...---......))))))))))))))))..)))).................................((.........)).. ( -15.74)
>consensus
UCCGCAUUUGCAUUAUUUUCGACUCAAGCA__AUA___UAAUUAGAGUCGAAAAAGGCGAACAUGCAACAAUUAUAUUUAAAUCAACUCACUCUUUUCCGCUAAAACCAUGCAU
...((((((((....((((((((((...................))))))))))..))))..)))).................................((.........)).. (-14.95 = -15.27 +   0.32)

alignment

secondary structure

dotplot

Window 5

Location	12,604,129 – 12,604,243
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	86.65
Mean single sequence MFE	-25.82
Consensus MFE	-18.55
Energy contribution	-19.15
Covariance contribution	0.60
Combinations/Pair	1.24
Mean z-score	-1.64
Structure conservation index	0.72
SVM decision value	0.03
SVM RNA-class probability	0.549469
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12604129 114 - 23771897
AUGCAUGGUUUUAGCGGAAAAGAGUGAGAUGAUUUAAAUAUAAUUGUUGCAUGUUCGCCUUUUUCGACUCUAAUUACUAUAUAUUGCUUGAGUCGAAAAUAAUGCAAAUGCGGA
.(((((.(((((...(((((((.((((((((.....((((....)))).))).))))))))))))(((((...................))))).))))).)))))........ ( -26.61)
>DroSec_CAF1 92006 111 - 1
AUGCAUGGUUUUAGCGGAAAAGAGUGCGAUGAUUUAAAUAUAAUUGUUGCAUGUUCGCCUUUUUCGACUCUAAUUA---UAUACUUCUCGAGUCAAAAAUAAUGCAAAUGCGGA
.(((((.(((((.(((((.....((((((..(((.......)))..)))))).))))).......(((((......---..........))))).))))).)))))........ ( -28.49)
>DroSim_CAF1 94815 109 - 1
AUGCAUGGUUUUAGCGGAAAAGAGUGAGUAGAUUUAAAUAUAAUUGUUGCAUGUUCGCCUUUUUCGACUCUAAUUA---UAU--UUCUCGAGUCGAAAAUAAUGCAAAUGCGGA
.(((((.(((((...(((((((.(((((((......((((....))))...))))))))))))))(((((......---...--.....))))).))))).)))))........ ( -24.74)
>DroEre_CAF1 95267 107 - 1
AUGCAUGGUUUAAGCGGAAUUGAGUGAGGCGAUUUAAAUAUAGAAGUUGCAUGUUCGCCU--UUUGGCUUUAAUUA---UAU--UGCUUAAGUCGAAAAUAAUGCAAAUACGGA
.(((((.((((...(((..(((((..(.(((((((........)))))))......(((.--...)))........---..)--..))))).))).)))).)))))........ ( -24.70)
>DroYak_CAF1 95664 109 - 1
UUGCAUGGCUUAAGCGGAAUAGAGUGAGUUUAUUUAAAUAUAGAUGUUGCAUGCUUGCCUAUUUUGACUUUAAUUA---UAU--UGCUUAAGUCGAAAAUAAUGCAAAUGCGGA
((((((((((((((((((((((.(..(((.((((((....))))))......)))..)))))))............---...--)))))))))).......))))))....... ( -24.57)
>consensus
AUGCAUGGUUUUAGCGGAAAAGAGUGAGAUGAUUUAAAUAUAAUUGUUGCAUGUUCGCCUUUUUCGACUCUAAUUA___UAU__UGCUUGAGUCGAAAAUAAUGCAAAUGCGGA
.(((((.......(((((.....(((.(((((((.......))))))).))).)))))...(((((((((...................)))))))))...)))))........ (-18.55 = -19.15 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:18:51 2006