Locus 2473

Sequence ID	3L_DroMel_CAF1
Location	6,975,099 – 6,975,327
Length	228
Max. P	0.957111

overview

Window 6

Location	6,975,099 – 6,975,218
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.98
Mean single sequence MFE	-30.33
Consensus MFE	-25.57
Energy contribution	-25.93
Covariance contribution	0.36
Combinations/Pair	1.08
Mean z-score	-1.43
Structure conservation index	0.84
SVM decision value	0.21
SVM RNA-class probability	0.634603
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6975099 119 + 23771897
UAAUUAAAUGACAAAUGCCCCGAAUUUGGCAGGGAAAAAAGUUGUGACAGCAAACAUUUUUGCCGCACAUUUGUGUUAACAUUCGUGGGCUUGACUGUUGAAAGUUUCCCCUUUUGUUG-
.........((((((((((........))))((((((...((((...)))).((((.((..(((.(((...(((....)))...))))))..)).)))).....))))))..)))))).- ( -30.80)
>DroSec_CAF1 45006 119 + 1
UAAUUAAAUGACAAAUGCCCCGAAUUUGGCAGGGAAAAAAGUUGUGACAGCAAACAUUUUUGCCACACAUUUGUGUUAACAUUCGUGGGCUUGACUGUUGAAAGUUUCCCCUUUUGUUG-
.........((((((((((........))))((((((...((((...)))).((((.((..(((.(((...(((....)))...))))))..)).)))).....))))))..)))))).- ( -30.80)
>DroSim_CAF1 44796 119 + 1
UAAUUAAAUGACAAAUGCCCCGAAUUUGGCAGGGAAAAAAGUUGUGACAGCAAACAUUUUUGCCACACAUUUGUGUUAACAUUCGUGGGCUUGACUGUUGAAAGUUUCCCCUUUUGUUG-
.........((((((((((........))))((((((...((((...)))).((((.((..(((.(((...(((....)))...))))))..)).)))).....))))))..)))))).- ( -30.80)
>DroEre_CAF1 44941 119 + 1
UAAUUAAAUGACAAAUGCCCCACAUUUGGCAGGGAAAAAAGUUGUGACAGCAAACAUUUUUGGCACACAUUUGUGUUAACAUUUGUGGGCUUGACUGUUGAAAGUUCCCCCUUUUGUUG-
.........((((((((((........))))(((((........(((((((((.((....))((.((((..(((....)))..)))).))))).))))))....)))))...)))))).- ( -30.40)
>DroYak_CAF1 46277 120 + 1
UAAUUAAAUGACAAAUGCCCCGAAUUUGGCUGGAAAAAAAGUUGUGACAGCAAACAUUUUUGGCACACAUUUGUGCUAACAUUCGUGGGCUUGACAGUUGAAAGUUCCCCCUUUUGUUGC
.........((((((.(((((((((...((((...............))))........((((((((....)))))))).))))).))))..(((........)))......)))))).. ( -28.86)
>consensus
UAAUUAAAUGACAAAUGCCCCGAAUUUGGCAGGGAAAAAAGUUGUGACAGCAAACAUUUUUGCCACACAUUUGUGUUAACAUUCGUGGGCUUGACUGUUGAAAGUUUCCCCUUUUGUUG_
.........((((((.(((((((((((((((.(((.......((((...(((((....)))))..))))))).)))))).))))).))))..((((......))))......)))))).. (-25.57 = -25.93 +   0.36)

alignment

secondary structure

dotplot

Window 7

Location	6,975,099 – 6,975,218
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.98
Mean single sequence MFE	-27.10
Consensus MFE	-23.78
Energy contribution	-23.90
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-1.54
Structure conservation index	0.88
SVM decision value	0.95
SVM RNA-class probability	0.887936
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6975099 119 - 23771897
-CAACAAAAGGGGAAACUUUCAACAGUCAAGCCCACGAAUGUUAACACAAAUGUGCGGCAAAAAUGUUUGCUGUCACAACUUUUUUCCCUGCCAAAUUCGGGGCAUUUGUCAUUUAAUUA
-..(((((((((((((.....((((.((........)).))))........(((((((((((....))))))).))))....))))))))(((........))).))))).......... ( -30.00)
>DroSec_CAF1 45006 119 - 1
-CAACAAAAGGGGAAACUUUCAACAGUCAAGCCCACGAAUGUUAACACAAAUGUGUGGCAAAAAUGUUUGCUGUCACAACUUUUUUCCCUGCCAAAUUCGGGGCAUUUGUCAUUUAAUUA
-..(((((((((((((......((((.(((((.......(((((.(((....)))))))).....)))))))))........))))))))(((........))).))))).......... ( -27.44)
>DroSim_CAF1 44796 119 - 1
-CAACAAAAGGGGAAACUUUCAACAGUCAAGCCCACGAAUGUUAACACAAAUGUGUGGCAAAAAUGUUUGCUGUCACAACUUUUUUCCCUGCCAAAUUCGGGGCAUUUGUCAUUUAAUUA
-..(((((((((((((......((((.(((((.......(((((.(((....)))))))).....)))))))))........))))))))(((........))).))))).......... ( -27.44)
>DroEre_CAF1 44941 119 - 1
-CAACAAAAGGGGGAACUUUCAACAGUCAAGCCCACAAAUGUUAACACAAAUGUGUGCCAAAAAUGUUUGCUGUCACAACUUUUUUCCCUGCCAAAUGUGGGGCAUUUGUCAUUUAAUUA
-..(((((((((..((......((((.(((((.......((...((((....))))..)).....)))))))))........))..))))(((........))).))))).......... ( -25.14)
>DroYak_CAF1 46277 120 - 1
GCAACAAAAGGGGGAACUUUCAACUGUCAAGCCCACGAAUGUUAGCACAAAUGUGUGCCAAAAAUGUUUGCUGUCACAACUUUUUUUCCAGCCAAAUUCGGGGCAUUUGUCAUUUAAUUA
...(((((((((....))))..........((((.(((((....(((((....)))))...........((((...............))))...))))))))).))))).......... ( -25.46)
>consensus
_CAACAAAAGGGGAAACUUUCAACAGUCAAGCCCACGAAUGUUAACACAAAUGUGUGGCAAAAAUGUUUGCUGUCACAACUUUUUUCCCUGCCAAAUUCGGGGCAUUUGUCAUUUAAUUA
...(((((((((....))))..........((((.(((((((....))...(((((((((((....))))))).)))).................))))))))).))))).......... (-23.78 = -23.90 +   0.12)

alignment

secondary structure

dotplot

Window 8

Location	6,975,139 – 6,975,248
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.51
Mean single sequence MFE	-23.88
Consensus MFE	-20.32
Energy contribution	-20.56
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.51
Structure conservation index	0.85
SVM decision value	0.75
SVM RNA-class probability	0.840395
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6975139 109 - 23771897
UAGAGUCGUCACACAGUGGCAACAAAAUCG-----------CAACAAAAGGGGAAACUUUCAACAGUCAAGCCCACGAAUGUUAACACAAAUGUGCGGCAAAAAUGUUUGCUGUCACAAC
....((.(((((...))))).)).......-----------.((((...((((..(((......)))....))).)...))))........(((((((((((....))))))).)))).. ( -24.30)
>DroSec_CAF1 45046 109 - 1
UAGAGUUGUCACACAGUGGCAACAAAAUCG-----------CAACAAAAGGGGAAACUUUCAACAGUCAAGCCCACGAAUGUUAACACAAAUGUGUGGCAAAAAUGUUUGCUGUCACAAC
..((((((((((...))))))))......(-----------(((((..((((....))))..........(((((((..(((....)))..)))).))).....)).))))..))..... ( -27.00)
>DroSim_CAF1 44836 109 - 1
UAGAGUCGUCACACAGUGGCAACAAAAUCG-----------CAACAAAAGGGGAAACUUUCAACAGUCAAGCCCACGAAUGUUAACACAAAUGUGUGGCAAAAAUGUUUGCUGUCACAAC
...............((((((.((((....-----------.......((((....))))..........(((((((..(((....)))..)))).))).......)))).))))))... ( -23.70)
>DroEre_CAF1 44981 106 - 1
UAGAG---CCACACAGUGGCAACAAAAUCG-----------CAACAAAAGGGGGAACUUUCAACAGUCAAGCCCACAAAUGUUAACACAAAUGUGUGCCAAAAAUGUUUGCUGUCACAAC
.....---.......((((((.((((....-----------.((((.....(((.(((......)))....))).....)))).((((....))))..........)))).))))))... ( -20.50)
>DroYak_CAF1 46317 117 - 1
UAGAG---UCACACAGUGGCAACAAAAUCGCAACACAAUCGCAACAAAAGGGGGAACUUUCAACUGUCAAGCCCACGAAUGUUAGCACAAAUGUGUGCCAAAAAUGUUUGCUGUCACAAC
.....---.......((((((.((((...(((.((((...((((((...(.(((.((........))....))).)...)))).)).....)))))))........)))).))))))... ( -23.90)
>consensus
UAGAGU_GUCACACAGUGGCAACAAAAUCG___________CAACAAAAGGGGAAACUUUCAACAGUCAAGCCCACGAAUGUUAACACAAAUGUGUGGCAAAAAUGUUUGCUGUCACAAC
...............((((((.((((......................((((....))))..........(((((((..(((....)))..)))).))).......)))).))))))... (-20.32 = -20.56 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	6,975,218 – 6,975,327
Length	109
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.63
Mean single sequence MFE	-28.06
Consensus MFE	-24.04
Energy contribution	-23.88
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.65
Structure conservation index	0.86
SVM decision value	1.23
SVM RNA-class probability	0.933294
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6975218 109 + 23771897
----------CGAUUUUGUUGCCACUGUGUGACGACUCUAAUUCACGGCAACAGCAACCGGCAGCGACAACUGGCCGAAAAGCAAAUGUACUUUGAUGUAAUACACAUAAACAUU-UGCA
----------.....((((((((.....((((..........))))))))))))....((((((......)).))))....((((((((....((.((.....))))...)))))-))). ( -27.90)
>DroSec_CAF1 45125 109 + 1
----------CGAUUUUGUUGCCACUGUGUGACAACUCUAAUUCACGGCAACAGCAACCGGCAGCGACAACUGGCCGAAAAGCAAAUGUACUUUGAUGUAAUACACAUAAACAUU-UGCA
----------.....((((((((.....((((..........))))))))))))....((((((......)).))))....((((((((....((.((.....))))...)))))-))). ( -27.90)
>DroSim_CAF1 44915 109 + 1
----------CGAUUUUGUUGCCACUGUGUGACGACUCUAAUUCACGGCAACAGCAACCGGCAGCGACAACUGGCCGAAAAGCAAAUGUACUUUGAUGUAAUAAACAUAAACAUU-UGCA
----------.....((((((((.....((((..........))))))))))))....((((((......)).))))....((((((((......((((.....))))..)))))-))). ( -28.10)
>DroEre_CAF1 45060 106 + 1
----------CGAUUUUGUUGCCACUGUGUGG---CUCUAAUUCACGGCAACAGCAACCGGCAGCGACAACUGGCCGAAAAGCAAAUGUACUUUGAUGUAAUACACAUAAACAUU-UGCA
----------.....((((((((.....((((---.......))))))))))))....((((((......)).))))....((((((((....((.((.....))))...)))))-))). ( -27.60)
>DroYak_CAF1 46397 117 + 1
GAUUGUGUUGCGAUUUUGUUGCCACUGUGUGA---CUCUAAUUCACGGCAACAGCAACCGGCAGCGACAACUGGCCGAAAAGCAAAUGUACUUUGAUGUAAUACACAUAAACAUUUUGCA
......(((((.....(((((((.....((((---.......))))))))))))))))((((((......)).))))....((((((((....((.((.....))))...))).))))). ( -28.80)
>consensus
__________CGAUUUUGUUGCCACUGUGUGAC_ACUCUAAUUCACGGCAACAGCAACCGGCAGCGACAACUGGCCGAAAAGCAAAUGUACUUUGAUGUAAUACACAUAAACAUU_UGCA
...............((((((((.....((((..........))))))))))))....((((((......)).))))....((((((((......((((.....))))..))))).))). (-24.04 = -23.88 +  -0.16)

alignment

secondary structure

dotplot

Window 0

Location	6,975,218 – 6,975,327
Length	109
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.63
Mean single sequence MFE	-31.86
Consensus MFE	-27.22
Energy contribution	-27.42
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.76
Structure conservation index	0.85
SVM decision value	1.47
SVM RNA-class probability	0.957111
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6975218 109 - 23771897
UGCA-AAUGUUUAUGUGUAUUACAUCAAAGUACAUUUGCUUUUCGGCCAGUUGUCGCUGCCGGUUGCUGUUGCCGUGAAUUAGAGUCGUCACACAGUGGCAACAAAAUCG----------
.(((-(((((....(((.....)))......))))))))....((((.(((....)))))))(((((..(((..((((..........)))).)))..))))).......---------- ( -32.30)
>DroSec_CAF1 45125 109 - 1
UGCA-AAUGUUUAUGUGUAUUACAUCAAAGUACAUUUGCUUUUCGGCCAGUUGUCGCUGCCGGUUGCUGUUGCCGUGAAUUAGAGUUGUCACACAGUGGCAACAAAAUCG----------
.(((-(((((....(((.....)))......))))))))....((((.(((....)))))))(((((..(((..((((..........)))).)))..))))).......---------- ( -32.30)
>DroSim_CAF1 44915 109 - 1
UGCA-AAUGUUUAUGUUUAUUACAUCAAAGUACAUUUGCUUUUCGGCCAGUUGUCGCUGCCGGUUGCUGUUGCCGUGAAUUAGAGUCGUCACACAGUGGCAACAAAAUCG----------
.(((-(((((..((((.....))))......))))))))....((((.(((....)))))))(((((..(((..((((..........)))).)))..))))).......---------- ( -32.30)
>DroEre_CAF1 45060 106 - 1
UGCA-AAUGUUUAUGUGUAUUACAUCAAAGUACAUUUGCUUUUCGGCCAGUUGUCGCUGCCGGUUGCUGUUGCCGUGAAUUAGAG---CCACACAGUGGCAACAAAAUCG----------
.(((-(((((....(((.....)))......))))))))....((((.(((....)))))))(((((..(((..(((........---.))).)))..))))).......---------- ( -31.20)
>DroYak_CAF1 46397 117 - 1
UGCAAAAUGUUUAUGUGUAUUACAUCAAAGUACAUUUGCUUUUCGGCCAGUUGUCGCUGCCGGUUGCUGUUGCCGUGAAUUAGAG---UCACACAGUGGCAACAAAAUCGCAACACAAUC
.............(((((..(((......)))....(((....((((.(((....)))))))(((((..(((..((((.......---)))).)))..)))))......))))))))... ( -31.20)
>consensus
UGCA_AAUGUUUAUGUGUAUUACAUCAAAGUACAUUUGCUUUUCGGCCAGUUGUCGCUGCCGGUUGCUGUUGCCGUGAAUUAGAGU_GUCACACAGUGGCAACAAAAUCG__________
.(((.(((((..((((.....))))......))))))))....((((.(((....)))))))(((((..(((..((((..........)))).)))..)))))................. (-27.22 = -27.42 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:15 2006