Locus 5921

Sequence ID	3L_DroMel_CAF1
Location	15,907,602 – 15,907,891
Length	289
Max. P	0.987756

overview

Window 1

Location	15,907,602 – 15,907,708
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.44
Mean single sequence MFE	-26.14
Consensus MFE	-16.29
Energy contribution	-16.89
Covariance contribution	0.60
Combinations/Pair	1.08
Mean z-score	-1.89
Structure conservation index	0.62
SVM decision value	0.68
SVM RNA-class probability	0.821587
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15907602 106 + 23771897
CUUUCUAGAAGGGUUUCUUUACA-AUUCUUCCUGGUUUAUAGC---------CUU----GCACGAAUGGGGAAAGAUCUGUACUGCGGAAAUUACCUAUCCGCCCACAGAACACCUCUCA
.......((..(((((((.((((-..(((((((.(((..(.((---------...----)))..))).))).))))..))))..(((((.........)))))....)))).)))..)). ( -27.30)
>DroSec_CAF1 7094 106 + 1
CUUUCUAGAAGGCUUUCUUUGCA-AUUCUUCCUGGUUUAUAGC---------CUU----GCAUGAAUGUGUAAAGAUCUGUACUGCGGAAAUUACCUAUCCGCCCACCGAACACCUCUCA
.......(((((...((((((((-((((.....(((.....))---------)..----....)))).))))))))((.((...(((((.........)))))..)).))...))).)). ( -23.10)
>DroSim_CAF1 9599 105 + 1
CUUUCUAGAAGGGUUUCUUUGCA-AUUCUUCCUGGUUUAUAGC----------UU----GCAUGAAUGUGUAAAGAUCUGUACUGCGGAAAUUACCUAUCCGCCCACCGAACACCUCUCA
.......((..(((.((((((((-((((.....(((.....))----------).----....)))).))))))))((.((...(((((.........)))))..)).))..)))..)). ( -24.60)
>DroEre_CAF1 7173 111 + 1
CUUUCUAGAAGGGUUG--UUCCCAUUUCUUCCUGGUU-----CACUUACAGCAAUAUAGACACGAAAAUGGAAAUAUCUGUAUGGCGGAAAUUACCAAUCCGCCCACAGAA--CCUCUCA
.......((..(((((--((.((((((..((.((...-----..................)).)))))))).))))(((((..((((((.........)))))).))))))--))..)). ( -26.50)
>DroYak_CAF1 7111 117 + 1
AUUUCUAGAAGUGUUUCUUUCCAAUUUCUUCCGGGUU-AUACCAUAUACAGCAAUAUUGACGCGAAAUGGGAAAGAUCUGUACUGCGGAAAUUACCAAUCCGCCCACAGAA--CCUCUCA
......(((.((...(((((((.(((((....((...-...)).......((.........))))))).)))))))(((((...(((((.........)))))..))))))--).))).. ( -29.20)
>consensus
CUUUCUAGAAGGGUUUCUUUCCA_AUUCUUCCUGGUUUAUAGC_________AUU____GCACGAAUGUGGAAAGAUCUGUACUGCGGAAAUUACCUAUCCGCCCACAGAACACCUCUCA
.......(((((...(((((((..((((...................................))))..)))))))(((((...(((((.........)))))..)))))...))).)). (-16.29 = -16.89 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	15,907,708 – 15,907,811
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.57
Mean single sequence MFE	-32.36
Consensus MFE	-22.07
Energy contribution	-22.12
Covariance contribution	0.05
Combinations/Pair	1.08
Mean z-score	-1.81
Structure conservation index	0.68
SVM decision value	0.12
SVM RNA-class probability	0.594739
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15907708 103 - 23771897
GAGGCAGGUGGGCUAAUUUCUAUAUGCCAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCG-----------------AUGUCGCAAAUGAAAGGGUGAUGGGGCAAGG
((((((((((.((((.((.((((((...)))))).)).))))...))))))))))....((.((((...((.-----------------...(((....)))..))...)))).)).... ( -28.90)
>DroSec_CAF1 7200 120 - 1
GGGGCAGGUGGGCUAAUUUCUAGAUGCCAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCGCAUAAGUUAUGACUGGGAUGUCGCAAGUGGAAGGGUGAUGGGGCAAGG
((((((((((..(((.....))).((((((.......))))))..)))))))))).....((((....(((((...(.((.((((......)))).)).)......)))))..))))... ( -33.60)
>DroSim_CAF1 9704 120 - 1
GGGGCAGGUGGGCUAAUUUCUAGAUGCCAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCGCCUAAGUUAUGACUGGGAUGUCGCAAAUGGAAGGGUGAUGGGGCAAGG
((((((((((..(((.....))).((((((.......))))))..)))))))))).....((((....(((((((..(((.((((......))))..)))....)))))))..))))... ( -37.20)
>DroEre_CAF1 7284 107 - 1
GGGGCAGGUGGGUUAAUUUCUAUUUGCUAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCGCUUAGGUUAUGACUGGGAUGUCGCAAGUGGAAG-------------GG
((((((((((..(......(((((((((....))))))))).)..))))))))))......(((((((.((.....)))))))))((.(....).))........-------------.. ( -29.60)
>DroYak_CAF1 7228 119 - 1
GGGGCAGGUGGGCUAAUUUCUAUAUGCUAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCGCUUAAGUUAUGACUGGGAUGUCGCAAAUGGAAGGGC-AUGGGGCGGGG
((((((((((.((((.((.((((((...)))))).)).))))...))))))))))......(((((((..........))))))).......((((..(((......)-))...)))).. ( -32.50)
>consensus
GGGGCAGGUGGGCUAAUUUCUAUAUGCCAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCGCUUAAGUUAUGACUGGGAUGUCGCAAAUGGAAGGGUGAUGGGGCAAGG
((((((((((.........((((.((((....)))).))))....))))))))))....(((.(((......(.........)......))).)))........................ (-22.07 = -22.12 +   0.05)

alignment

secondary structure

dotplot

Window 3

Location	15,907,739 – 15,907,851
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.00
Mean single sequence MFE	-31.74
Consensus MFE	-26.98
Energy contribution	-26.98
Covariance contribution	0.00
Combinations/Pair	1.07
Mean z-score	-2.07
Structure conservation index	0.85
SVM decision value	2.09
SVM RNA-class probability	0.987756
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15907739 112 - 23771897
UGUAAAAACUUGACAAAUGUGAAAACAUCAUCGACAGGCAGAGGCAGGUGGGCUAAUUUCUAUAUGCCAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCG--------
..........(((((.((((....))))............((((((((((.((((.((.((((((...)))))).)).))))...)))))))))).....))))).......-------- ( -30.10)
>DroSec_CAF1 7240 120 - 1
UGUAAAAACUUGACAAAUGUGAAAACAUCAUCGACAGGCAGGGGCAGGUGGGCUAAUUUCUAGAUGCCAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCGCAUAAGUU
......((((((....((((....))))....((((....((((((((((..(((.....))).((((((.......))))))..)))))))))).....))))..........)))))) ( -31.30)
>DroSim_CAF1 9744 120 - 1
UGUAAAAACUUGACAAAUGUGAAAACAUCAUCGACAGGCAGGGGCAGGUGGGCUAAUUUCUAGAUGCCAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCGCCUAAGUU
......(((((((...((((....))))..))...((((.((((((((((..(((.....))).((((((.......))))))..))))))))))((.....)).......))))))))) ( -32.10)
>DroEre_CAF1 7311 119 - 1
UGUAA-AACUUGACAAAUGUGAAAACAUCACCGACAGGCAGGGGCAGGUGGGUUAAUUUCUAUUUGCUAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCGCUUAGGUU
.....-((((((((..((((....))))....((((....((((((((((..(......(((((((((....))))))))).)..)))))))))).....)))).......).))))))) ( -32.80)
>DroYak_CAF1 7267 120 - 1
UGUAAAAACUUGACAAAUGUGAAAACAUCAUCGACAGGCAGGGGCAGGUGGGCUAAUUUCUAUAUGCUAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCGCUUAAGUU
......((((((((..((((....))))....((((....((((((((((.((((.((.((((((...)))))).)).))))...)))))))))).....)))).......).))))))) ( -32.40)
>consensus
UGUAAAAACUUGACAAAUGUGAAAACAUCAUCGACAGGCAGGGGCAGGUGGGCUAAUUUCUAUAUGCCAUGUGGUAAAUGGUAAACAUCUGCUUCGAAAGUGUCAUAAAUCGCUUAAGUU
..........(((((.((((....))))............((((((((((.........((((.((((....)))).))))....)))))))))).....)))))............... (-26.98 = -26.98 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	15,907,771 – 15,907,891
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.17
Mean single sequence MFE	-35.30
Consensus MFE	-31.20
Energy contribution	-31.04
Covariance contribution	-0.16
Combinations/Pair	1.11
Mean z-score	-1.20
Structure conservation index	0.88
SVM decision value	0.07
SVM RNA-class probability	0.566747
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15907771 120 - 23771897
GAUCACGCCCCCACCACUUGGCGGUCUUGUAAAGCUGCAGUGUAAAAACUUGACAAAUGUGAAAACAUCAUCGACAGGCAGAGGCAGGUGGGCUAAUUUCUAUAUGCCAUGUGGUAAAUG
.((((((((.....((((..(((((........))))))))).......((((...((((....))))..))))..)))...((((.(((((......))))).))))..)))))..... ( -32.00)
>DroSec_CAF1 7280 120 - 1
GAUCACGCCCCCACCACUUGGCGGUCUUGUAAAGCUGCGAUGUAAAAACUUGACAAAUGUGAAAACAUCAUCGACAGGCAGGGGCAGGUGGGCUAAUUUCUAGAUGCCAUGUGGUAAAUG
.((((((((((..((((.(.(((((........))))).).))......((((...((((....))))..))))..))..))))).((((..(((.....))).))))..)))))..... ( -35.10)
>DroSim_CAF1 9784 120 - 1
GAUCACGCCCCCACCACUUGGCGGUCUUGUAAAGCUGCGAUGUAAAAACUUGACAAAUGUGAAAACAUCAUCGACAGGCAGGGGCAGGUGGGCUAAUUUCUAGAUGCCAUGUGGUAAAUG
.((((((((((..((((.(.(((((........))))).).))......((((...((((....))))..))))..))..))))).((((..(((.....))).))))..)))))..... ( -35.10)
>DroEre_CAF1 7351 119 - 1
GACCACGCCCCCACCACUUUGCGGUCUUGUAAGGCUGCAGUGUAA-AACUUGACAAAUGUGAAAACAUCACCGACAGGCAGGGGCAGGUGGGUUAAUUUCUAUUUGCUAUGUGGUAAAUG
.((((((((((..((((.(((((((((....))))))))).))..-..........((((....))))........))..))))).((..(((........)))..))..)))))..... ( -40.60)
>DroYak_CAF1 7307 120 - 1
GAUCACGCCCCCACCACUUUGCGGUCUUGUAAAGCUGCAGUGUAAAAACUUGACAAAUGUGAAAACAUCAUCGACAGGCAGGGGCAGGUGGGCUAAUUUCUAUAUGCUAUGUGGUAAAUG
.((((((((((..((((.(((((((........))))))).))......((((...((((....))))..))))..))..)))))..(((((......))))).......)))))..... ( -33.70)
>consensus
GAUCACGCCCCCACCACUUGGCGGUCUUGUAAAGCUGCAGUGUAAAAACUUGACAAAUGUGAAAACAUCAUCGACAGGCAGGGGCAGGUGGGCUAAUUUCUAUAUGCCAUGUGGUAAAUG
.((((((((((..((.....(((((........)))))...........((((...((((....))))..))))..))..))))).....(((............)))..)))))..... (-31.20 = -31.04 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:06 2006