Locus 3516

Sequence ID	X_DroMel_CAF1
Location	9,430,373 – 9,430,549
Length	176
Max. P	0.999986

overview

Window 6

Location	9,430,373 – 9,430,481
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.53
Mean single sequence MFE	-33.70
Consensus MFE	-20.55
Energy contribution	-20.88
Covariance contribution	0.34
Combinations/Pair	1.27
Mean z-score	-2.37
Structure conservation index	0.61
SVM decision value	1.64
SVM RNA-class probability	0.969342
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9430373 108 - 22224390
UCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAUUUGGCUGAUAU----UGACACCCUACAAACUGUGGGGU------GCAAUGGAAUUU-CUGUGGCACAGAAAUG-UAUUAU
(((((((......)))).((.....((((..((((((......))))))..----))))(((((((.....)))))))------))...)))((((-(((.....))))))).-...... ( -38.20)
>DroSec_CAF1 12136 107 - 1
UCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAUUUGGCUGAUAU----UGACACCCUACUAACUGUGGGGU------GCAAUGGAAUUU-CUGUGACAUACAUAUG-UUUU-U
(((((((......)))).((.....((((..((((((......))))))..----))))(((((((.....)))))))------))...)))....-....(((((....)))-))..-. ( -33.50)
>DroSim_CAF1 12851 107 - 1
UCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAUUUGGCUGAUAU----UGACACCCUACAAACUGUGGGGU------GCAAUGGAAUUU-CUGUGACACACAUAUG-UUUU-U
(((((((......)))).((.....((((..((((((......))))))..----))))(((((((.....)))))))------))...)))....-.((((...))))....-....-. ( -32.80)
>DroEre_CAF1 12306 112 - 1
UCCGCUUAUGAGAGAGCCGCGGUUUGUCGUCGUCAGCAAUUUGGCUGAUAUAUAUGUACACCCUACAAACUGUGGGGU------GCAAUGGAAUUU-CAUUGGCACACAUAUAGUUUU-U
.((((.............)))).........((((((......)))))).(((((((.((((((((.....)))))))------)((((((....)-)))))....))))))).....-. ( -35.12)
>DroYak_CAF1 12795 108 - 1
UCCGCUUAUGAGAGAGCCGCAUUUUGUCGUCGUCAGCAAUUUGGCUGAUAU----UGACACCCUACAAACUGUGGGGU------GCAAUGGAAUUU-CUUUGGCACACAUAUACUUUU-U
...(((...((((((..(.((((..((((..((((((......))))))..----))))(((((((.....)))))))------..)))))..)))-))).)))..............-. ( -35.00)
>DroAna_CAF1 9556 100 - 1
-GAGCUCA--AGAGAGUUCAUAUUUGCUUUCGUCAGCAU----------A-----UGAUACCCUACCUCCAGUGGGGUUGUUCGGCACUAGGAGUUAGUGGGUUUCA-AAAUC-GAAAAU
-((((((.--...)))))).....((((......)))).----------.-----(((.((((...((((((((..(.....)..)))).)))).....)))).)))-.....-...... ( -27.60)
>consensus
UCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAUUUGGCUGAUAU____UGACACCCUACAAACUGUGGGGU______GCAAUGGAAUUU_CUGUGGCACACAUAUG_UUUU_U
...((((......)))).......(((((..((((((......))))))..........(((((((.....)))))))......................)))))............... (-20.55 = -20.88 +   0.34)

alignment

secondary structure

dotplot

Window 7

Location	9,430,407 – 9,430,519
Length	112
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	95.01
Mean single sequence MFE	-41.12
Consensus MFE	-37.02
Energy contribution	-37.42
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-3.03
Structure conservation index	0.90
SVM decision value	4.40
SVM RNA-class probability	0.999890
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9430407 112 + 22224390
ACCCCACAGUUUGUAGGGUGUCA----AUAUCAGCCAAAUUGCUGACGACGACAAAAGGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCCUUGUAGU--
((((.((.....)).))))(((.----...(((((......))))).))).((((..((((.(((((((....((....)).....)))))))))))(((....)))..))))...-- ( -41.50)
>DroSec_CAF1 12169 111 + 1
ACCCCACAGUUAGUAGGGUGUCA----AUAUCAGCCAAAUUGCUGACGACGACAAAAGGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCC-UGUAGU--
.............(((((((((.----...(((((......)))))....)))....((((((((((((....((....)).....))))))))..)))).....))))-))....-- ( -42.40)
>DroSim_CAF1 12884 111 + 1
ACCCCACAGUUUGUAGGGUGUCA----AUAUCAGCCAAAUUGCUGACGACGACAAAAGGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCC-UGUAGU--
..........((((((((((((.----...(((((......)))))....)))....((((((((((((....((....)).....))))))))..)))).....))))-))))).-- ( -42.70)
>DroEre_CAF1 12340 116 + 1
ACCCCACAGUUUGUAGGGUGUACAUAUAUAUCAGCCAAAUUGCUGACGACGACAAACCGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCAUUGUAGU--
((((.((.....)).)))).((((......(((((......))))).((((......)...((((((((....((....)).....)))))))))))(((....)))...))))..-- ( -38.60)
>DroYak_CAF1 12829 114 + 1
ACCCCACAGUUUGUAGGGUGUCA----AUAUCAGCCAAAUUGCUGACGACGACAAAAUGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCCUUGUAGUUG
((((.((.....)).))))....----...(((((......)))))((((.((((......((((((((....((....)).....))))))))...(((....)))..)))).)))) ( -40.40)
>consensus
ACCCCACAGUUUGUAGGGUGUCA____AUAUCAGCCAAAUUGCUGACGACGACAAAAGGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCCUUGUAGU__
((((.((.....)).))))...........(((((......)))))..((.(((...((((.(((((((....((....)).....)))))))))))(((....)))...))).)).. (-37.02 = -37.42 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	9,430,407 – 9,430,519
Length	112
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	95.01
Mean single sequence MFE	-46.16
Consensus MFE	-44.08
Energy contribution	-44.68
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-3.81
Structure conservation index	0.95
SVM decision value	5.41
SVM RNA-class probability	0.999986
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9430407 112 - 22224390
--ACUACAAGGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAUUUGGCUGAUAU----UGACACCCUACAAACUGUGGGGU
--.....(((((((....)))...((((((((.....((....))....))))))))..))))..((((..((((((......))))))..----))))(((((((.....))))))) ( -46.50)
>DroSec_CAF1 12169 111 - 1
--ACUACA-GGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAUUUGGCUGAUAU----UGACACCCUACUAACUGUGGGGU
--....((-(...)))..((((..((((((((.....((....))....))))))))))))....((((..((((((......))))))..----))))(((((((.....))))))) ( -46.40)
>DroSim_CAF1 12884 111 - 1
--ACUACA-GGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAUUUGGCUGAUAU----UGACACCCUACAAACUGUGGGGU
--....((-(...)))..((((..((((((((.....((....))....))))))))))))....((((..((((((......))))))..----))))(((((((.....))))))) ( -46.20)
>DroEre_CAF1 12340 116 - 1
--ACUACAAUGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCGGUUUGUCGUCGUCAGCAAUUUGGCUGAUAUAUAUGUACACCCUACAAACUGUGGGGU
--..(((((((((..(((.(((..((((((((.....((....))....))))))))))).))).))))).((((((......)))))).....)))).(((((((.....))))))) ( -46.30)
>DroYak_CAF1 12829 114 - 1
CAACUACAAGGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCAUUUUGUCGUCGUCAGCAAUUUGGCUGAUAU----UGACACCCUACAAACUGUGGGGU
......((((...(((((((((((((((((((.....((....))....))))))))........)))))))))))...))))........----....(((((((.....))))))) ( -45.40)
>consensus
__ACUACAAGGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAUUUGGCUGAUAU____UGACACCCUACAAACUGUGGGGU
......((((...(((((((((((((((((((.....((....))....))))))))........)))))))))))...))))................(((((((.....))))))) (-44.08 = -44.68 +   0.60)

alignment

secondary structure

dotplot

Window 9

Location	9,430,441 – 9,430,549
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.64
Mean single sequence MFE	-34.25
Consensus MFE	-23.17
Energy contribution	-23.88
Covariance contribution	0.71
Combinations/Pair	1.24
Mean z-score	-1.67
Structure conservation index	0.68
SVM decision value	0.95
SVM RNA-class probability	0.888877
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9430441 108 + 22224390
AUUGCUGACGACGACAAAAGGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCCUUGUAGU------------UCCGCGUUUAUGGCACGAUAAGAACGAGAU
..((((((((..(((..((((..((((((((....((....)).....))))))))...(((....)))))))...))------------)...))))...))))............... ( -34.70)
>DroSec_CAF1 12203 107 + 1
AUUGCUGACGACGACAAAAGGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCC-UGUAGU------------UCCGCGUUUAUGGCACGAUAAGAAUGAGAU
..((((((((..(((....((((.(((((((....((....)).....)))))))))))(((....)))..-....))------------)...))))...))))............... ( -34.30)
>DroSim_CAF1 12918 107 + 1
AUUGCUGACGACGACAAAAGGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCC-UGUAGU------------UCUGCGUUUAUGGCACGAUAAGAAUGAGAU
..((((((((..(((....((((.(((((((....((....)).....)))))))))))(((....)))..-....))------------)...))))...))))............... ( -34.30)
>DroEre_CAF1 12378 108 + 1
AUUGCUGACGACGACAAACCGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCAUUGUAGU------------UCCGCGUUUAUGGCGUGAUAAGAACGAGAU
..(((.((((.((......))).((((((((....((....)).....)))))))))))(((....)))....)))((------------(((((((.....)))))....))))..... ( -35.10)
>DroYak_CAF1 12863 120 + 1
AUUGCUGACGACGACAAAAUGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCCUUGUAGUUGUAGUUGUUCUUCCGCGUGUAUGGCAUGAUAAGAACGAGAU
...((((.((((.((((......((((((((....((....)).....))))))))...(((....)))..)))).))))))))(((((((...((((.....))))..))))))).... ( -42.00)
>DroAna_CAF1 9620 86 + 1
-AUGCUGACGAAAGCAAAUAUGAACUCUCU--UGAGCUC----------GGAGAGC---CCUUUUGGGGCC-UGUCGU------------UCA-----UGUAGGACAGUAAUGAUGAUAU
-.(((((.(....)...(((((((((((((--.......----------)))))((---((.....)))).-....))------------)))-----)))....))))).......... ( -25.10)
>consensus
AUUGCUGACGACGACAAAAGGCGGCUCUCUCAUAAGCGGAAGCAAAAAGAGAGAGCGUCGCCGCCAGGCCC_UGUAGU____________UCCGCGUUUAUGGCACGAUAAGAACGAGAU
..((((...((((..........((((((((....((....)).....))))))))...(((....))).........................))))...))))............... (-23.17 = -23.88 +   0.71)

alignment

secondary structure

dotplot

Window 0

Location	9,430,441 – 9,430,549
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.64
Mean single sequence MFE	-34.94
Consensus MFE	-25.13
Energy contribution	-26.28
Covariance contribution	1.15
Combinations/Pair	1.14
Mean z-score	-2.55
Structure conservation index	0.72
SVM decision value	1.88
SVM RNA-class probability	0.981305
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9430441 108 - 22224390
AUCUCGUUCUUAUCGUGCCAUAAACGCGGA------------ACUACAAGGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAU
.....(((((...(((.......))).)))------------)).......((.((((((((((((((((((.....((....))....))))))))........))))))))))))... ( -38.60)
>DroSec_CAF1 12203 107 - 1
AUCUCAUUCUUAUCGUGCCAUAAACGCGGA------------ACUACA-GGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAU
............(((((.......))))).------------......-..((.((((((((((((((((((.....((....))....))))))))........))))))))))))... ( -36.40)
>DroSim_CAF1 12918 107 - 1
AUCUCAUUCUUAUCGUGCCAUAAACGCAGA------------ACUACA-GGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAU
......((((...(((.......))).)))------------).....-..((.((((((((((((((((((.....((....))....))))))))........))))))))))))... ( -35.20)
>DroEre_CAF1 12378 108 - 1
AUCUCGUUCUUAUCACGCCAUAAACGCGGA------------ACUACAAUGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCGGUUUGUCGUCGUCAGCAAU
................(((((.........------------......)))))(((((((((((((((((((.....((....))....))))))))........))))))))))).... ( -36.76)
>DroYak_CAF1 12863 120 - 1
AUCUCGUUCUUAUCAUGCCAUACACGCGGAAGAACAACUACAACUACAAGGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCAUUUUGUCGUCGUCAGCAAU
.....((((((....(((.......))).))))))................((.((((((((((((((((((.....((....))....))))))))........))))))))))))... ( -40.60)
>DroAna_CAF1 9620 86 - 1
AUAUCAUCAUUACUGUCCUACA-----UGA------------ACGACA-GGCCCCAAAAGG---GCUCUCC----------GAGCUCA--AGAGAGUUCAUAUUUGCUUUCGUCAGCAU-
............(((((.....-----...------------..))))-)((((.....))---)).....----------((((((.--...)))))).....((((......)))).- ( -22.10)
>consensus
AUCUCAUUCUUAUCGUGCCAUAAACGCGGA____________ACUACA_GGGCCUGGCGGCGACGCUCUCUCUUUUUGCUUCCGCUUAUGAGAGAGCCGCCUUUUGUCGUCGUCAGCAAU
.....................................................(((((((((((((((((((.....((....))....))))))))........))))))))))).... (-25.13 = -26.28 +   1.15)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:24 2006