Locus 2942

Sequence ID	3R_DroMel_CAF1
Location	7,871,985 – 7,872,171
Length	186
Max. P	0.999551

overview

Window 6

Location	7,871,985 – 7,872,091
Length	106
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	86.33
Mean single sequence MFE	-30.79
Consensus MFE	-24.69
Energy contribution	-24.25
Covariance contribution	-0.44
Combinations/Pair	1.20
Mean z-score	-1.98
Structure conservation index	0.80
SVM decision value	0.19
SVM RNA-class probability	0.625322
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7871985 106 - 27905053
UCUGUCCCUAU------AUUCCAGUAUUCAUGCCAAAUUCUUAGCUGCUGACAAUUUGGCGUGACUGGGAAUGAAAACCAGGC-----ACU---UCGCUUGUACUUGAUGGAAAGUUUGC
((((((.....------.((((((...((((((((((((.((((...)))).))))))))))))))))))........(((((-----...---..))))).....))))))........ ( -33.60)
>DroSec_CAF1 3777 106 - 1
UCUGUCUUUAU------AUUCCGGUAUUCAUGCCAAAUUCUUAGCUGCUGACAAUUUGGCGUGACUGGGAAUGAAAACCAGGC-----ACU---UCGCUCGUACUUGAUGGAAAGUUUGC
...((.(((((------.((((((...((((((((((((.((((...)))).))))))))))))))))))))))).))(((((-----..(---(((.(((....)))))))..))))). ( -31.10)
>DroSim_CAF1 3784 106 - 1
UCUGUCUUUAU------AUUCCGGUAUUCAUGCCAAAUUCUUAGCUGCUGACAAUUUGGCGUGACUGGGAAUGAAAACCAGGC-----ACU---UCGCUCGUACUUGAUGGAAAGUUUGC
...((.(((((------.((((((...((((((((((((.((((...)))).))))))))))))))))))))))).))(((((-----..(---(((.(((....)))))))..))))). ( -31.10)
>DroEre_CAF1 3834 106 - 1
GCUGUCUUUUA------AUUCUGGUAUUCAUGCCAAAUUCUUAGCUGCUGACAAUUUGGCGUGACUGGGAAUGAAAACCAGGC-----ACU---UCGCAUGUACUUGAUGGAAAGUUUGC
((...(((((.------..((.(((((((((((((((((.((((...)))).))))))))))))((((.........))))((-----...---..))..))))).))..)))))...)) ( -32.60)
>DroYak_CAF1 3795 106 - 1
CCUCUCCUUUA------AUUCCGGUAUUCAUGCCAAAUUCUUAGCUUCUGACAAUUUGGCGUGACUGGGAAUGAAAACCAGGC-----ACU---UCGCUUGUACUUGAUGGAAAGUUUGC
.((.(((((((------.((((((...((((((((((((.((((...)))).)))))))))))))))))).))))...(((((-----...---..)))))........))).))..... ( -33.30)
>DroAna_CAF1 1241 119 - 1
UCUUUCUUUAUUUUGCCGUUCUGUUUUUCAUGCAAAAUUUUUAGCUGUUGACAAUUUGGCGUGACUCGUAAUGAAAGCCAGGCGAAGUACUACACUGCGUAUACUUGACGGGAAGUUU-C
.(((((..(((((((((.(((......((((((.(((((.((((...)))).))))).))))))........))).....)))))))))........(((.......))))))))...-. ( -23.04)
>consensus
UCUGUCUUUAU______AUUCCGGUAUUCAUGCCAAAUUCUUAGCUGCUGACAAUUUGGCGUGACUGGGAAUGAAAACCAGGC_____ACU___UCGCUUGUACUUGAUGGAAAGUUUGC
..................(((((....((((((((((((.((((...)))).))))))))))))((((.........))))...........................)))))....... (-24.69 = -24.25 +  -0.44)

alignment

secondary structure

dotplot

Window 7

Location	7,872,017 – 7,872,131
Length	114
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	93.77
Mean single sequence MFE	-32.72
Consensus MFE	-28.58
Energy contribution	-28.42
Covariance contribution	-0.16
Combinations/Pair	1.10
Mean z-score	-1.38
Structure conservation index	0.87
SVM decision value	0.62
SVM RNA-class probability	0.802327
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7872017 114 + 27905053
UGGUUUUCAUUCCCAGUCACGCCAAAUUGUCAGCAGCUAAGAAUUUGGCAUGAAUACUGGAAUAUAGGGACAGAAGGACUCAUCCAAAGGGCUGGAGACAGUACCAGCCUGGCG
..((((..((..(((((((.((((((((.(.((...)).).)))))))).)))...))))...))..))))....(((....)))...(((((((........))))))).... ( -33.80)
>DroSec_CAF1 3809 114 + 1
UGGUUUUCAUUCCCAGUCACGCCAAAUUGUCAGCAGCUAAGAAUUUGGCAUGAAUACCGGAAUAUAAAGACAGAACGACUCCUCCAAAGGGCUGGAGACAGUACCAGCCUGGCG
..(((((.(((((...(((.((((((((.(.((...)).).)))))))).))).....)))))...))))).................(((((((........))))))).... ( -30.80)
>DroSim_CAF1 3816 114 + 1
UGGUUUUCAUUCCCAGUCACGCCAAAUUGUCAGCAGCUAAGAAUUUGGCAUGAAUACCGGAAUAUAAAGACAGAACGACUCCUCCAAAGGGCUGGAGACAGUACCAGCCUGGCG
..(((((.(((((...(((.((((((((.(.((...)).).)))))))).))).....)))))...))))).................(((((((........))))))).... ( -30.80)
>DroEre_CAF1 3866 114 + 1
UGGUUUUCAUUCCCAGUCACGCCAAAUUGUCAGCAGCUAAGAAUUUGGCAUGAAUACCAGAAUUAAAAGACAGCACGACUCUUCCAAAGGGCUGGAGACAGUACCAGCUUGUCG
((((.(((((..........((((((((.(.((...)).).))))))))))))).)))).........((((((..((....))....((((((....)))).)).)).)))). ( -30.30)
>DroYak_CAF1 3827 114 + 1
UGGUUUUCAUUCCCAGUCACGCCAAAUUGUCAGAAGCUAAGAAUUUGGCAUGAAUACCGGAAUUAAAGGAGAGGACGACUCUUCCAAAGGGCUGGAGACAGUCCCAGCCUGUCG
.((((((.(((((...(((.((((((((.(.((...)).).)))))))).))).....))))).)))((((((.....))))))....((((((....))))))..)))..... ( -37.90)
>consensus
UGGUUUUCAUUCCCAGUCACGCCAAAUUGUCAGCAGCUAAGAAUUUGGCAUGAAUACCGGAAUAUAAAGACAGAACGACUCCUCCAAAGGGCUGGAGACAGUACCAGCCUGGCG
..(((((.(((((...(((.((((((((.(.((...)).).)))))))).))).....)))))...))))).................(((((((........))))))).... (-28.58 = -28.42 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	7,872,017 – 7,872,131
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	93.77
Mean single sequence MFE	-39.00
Consensus MFE	-33.78
Energy contribution	-33.66
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-2.84
Structure conservation index	0.87
SVM decision value	3.71
SVM RNA-class probability	0.999551
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7872017 114 - 27905053
CGCCAGGCUGGUACUGUCUCCAGCCCUUUGGAUGAGUCCUUCUGUCCCUAUAUUCCAGUAUUCAUGCCAAAUUCUUAGCUGCUGACAAUUUGGCGUGACUGGGAAUGAAAACCA
.....((((((........))))))....((((.((.....)))))).....((((((...((((((((((((.((((...)))).)))))))))))))))))).......... ( -38.30)
>DroSec_CAF1 3809 114 - 1
CGCCAGGCUGGUACUGUCUCCAGCCCUUUGGAGGAGUCGUUCUGUCUUUAUAUUCCGGUAUUCAUGCCAAAUUCUUAGCUGCUGACAAUUUGGCGUGACUGGGAAUGAAAACCA
..(((((((((........))))))...))).((..(((((((((....)))..((((...((((((((((((.((((...)))).))))))))))))))))))))))...)). ( -39.90)
>DroSim_CAF1 3816 114 - 1
CGCCAGGCUGGUACUGUCUCCAGCCCUUUGGAGGAGUCGUUCUGUCUUUAUAUUCCGGUAUUCAUGCCAAAUUCUUAGCUGCUGACAAUUUGGCGUGACUGGGAAUGAAAACCA
..(((((((((........))))))...))).((..(((((((((....)))..((((...((((((((((((.((((...)))).))))))))))))))))))))))...)). ( -39.90)
>DroEre_CAF1 3866 114 - 1
CGACAAGCUGGUACUGUCUCCAGCCCUUUGGAAGAGUCGUGCUGUCUUUUAAUUCUGGUAUUCAUGCCAAAUUCUUAGCUGCUGACAAUUUGGCGUGACUGGGAAUGAAAACCA
((((..(((((........)))))((...))....))))....(..(((((.(((..(...((((((((((((.((((...)))).)))))))))))))..))).)))))..). ( -35.30)
>DroYak_CAF1 3827 114 - 1
CGACAGGCUGGGACUGUCUCCAGCCCUUUGGAAGAGUCGUCCUCUCCUUUAAUUCCGGUAUUCAUGCCAAAUUCUUAGCUUCUGACAAUUUGGCGUGACUGGGAAUGAAAACCA
.....(((((((......)))))))....(((.(((.....))))))((((.((((((...((((((((((((.((((...)))).)))))))))))))))))).))))..... ( -41.60)
>consensus
CGCCAGGCUGGUACUGUCUCCAGCCCUUUGGAAGAGUCGUUCUGUCUUUAUAUUCCGGUAUUCAUGCCAAAUUCUUAGCUGCUGACAAUUUGGCGUGACUGGGAAUGAAAACCA
.....((((((........))))))...(((...((.....)).........((((((...((((((((((((.((((...)))).)))))))))))))))))).......))) (-33.78 = -33.66 +  -0.12)

alignment

secondary structure

dotplot

Window 9

Location	7,872,057 – 7,872,171
Length	114
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	93.77
Mean single sequence MFE	-33.56
Consensus MFE	-27.94
Energy contribution	-28.82
Covariance contribution	0.88
Combinations/Pair	1.06
Mean z-score	-2.06
Structure conservation index	0.83
SVM decision value	1.79
SVM RNA-class probability	0.977139
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7872057 114 - 27905053
UAAUUGGUAUGGACCACUUAGUUAAUGAAAUUGAAGCUGCCGCCAGGCUGGUACUGUCUCCAGCCCUUUGGAUGAGUCCUUCUGUCCCUAUAUUCCAGUAUUCAUGCCAAAUUC
...((((((((((..(((..............((((..(((((((((((((........))))))...))).)).)).))))..............))).)))))))))).... ( -30.19)
>DroSec_CAF1 3849 114 - 1
UAAUUGGUAUGGACCACUUAGUUAAUGAAACUGAAGCUGCCGCCAGGCUGGUACUGUCUCCAGCCCUUUGGAGGAGUCGUUCUGUCUUUAUAUUCCGGUAUUCAUGCCAAAUUC
...((((((((((((..((((((.....)))))).(((.((.(((((((((........))))))...))).)))))...................)))..))))))))).... ( -35.30)
>DroSim_CAF1 3856 114 - 1
UAAUUGGUAUGGACCACUUAGUUAAUGAAAUUGAAGCUGCCGCCAGGCUGGUACUGUCUCCAGCCCUUUGGAGGAGUCGUUCUGUCUUUAUAUUCCGGUAUUCAUGCCAAAUUC
...((((((((((((.......(((.((....((((((.((.(((((((((........))))))...))).)))))..)))..)).)))......)))..))))))))).... ( -33.02)
>DroEre_CAF1 3906 114 - 1
UAAUUGGUAUGGACCACUUAGUUAAUGAAAUUGAAGCUGCCGACAAGCUGGUACUGUCUCCAGCCCUUUGGAAGAGUCGUGCUGUCUUUUAAUUCUGGUAUUCAUGCCAAAUUC
...(((((((((((((...((((((.((...(((..((.((((...(((((........)))))...)))).))..))).....))..)))))).))))..))))))))).... ( -32.80)
>DroYak_CAF1 3867 114 - 1
UAAUUGGUAUGGACCACUUAGUUAAUGAAAUUGAAGCUGCCGACAGGCUGGGACUGUCUCCAGCCCUUUGGAAGAGUCGUCCUCUCCUUUAAUUCCGGUAUUCAUGCCAAAUUC
...((((((((((..(((.((((((.((...(((..((.((((..(((((((......)))))))..)))).))..)))...))....))))))..))).)))))))))).... ( -36.50)
>consensus
UAAUUGGUAUGGACCACUUAGUUAAUGAAAUUGAAGCUGCCGCCAGGCUGGUACUGUCUCCAGCCCUUUGGAAGAGUCGUUCUGUCUUUAUAUUCCGGUAUUCAUGCCAAAUUC
...((((((((((..(((....(((.((...(((..((.(((...((((((........))))))...))).))..))).....)).)))......))).)))))))))).... (-27.94 = -28.82 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:23 2006