Locus 2583

Sequence ID	3L_DroMel_CAF1
Location	7,196,002 – 7,196,176
Length	174
Max. P	0.922595

overview

Window 4

Location	7,196,002 – 7,196,121
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.48
Mean single sequence MFE	-40.18
Consensus MFE	-36.28
Energy contribution	-36.68
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.18
Structure conservation index	0.90
SVM decision value	0.01
SVM RNA-class probability	0.538181
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7196002 119 + 23771897
UCCUGUCUU-CUGUAUCCUGUCCCGGAGCUGUCCUGUUCUCCUAGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCA
..((((.((-((((..((((..(.((((.(((((.((((........))))))))).)))).)..))))((((((.....)).....((((((.....)))))))))))))))))))).. ( -41.00)
>DroSec_CAF1 9581 119 + 1
UCCUGUCUU-CUGUAUCCUGUCCCGGCGCUGUCCUGUUCUCCUGGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCA
.........-((((.((((((...((((((((((.(((.....))).)))))).))))...((((.((((((......))))))...((((((.....)))))))))))))))))))).. ( -40.40)
>DroSim_CAF1 1501 119 + 1
UCCUGUCUU-CUGUAUCCUGUCCCGGUGCUGUCCUGUUCUCCUGGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCA
.........-................((((((((((((.((..(((..((((.((..((.......))..))))))....)))....((((((.....)))))))).)))))).)))))) ( -38.40)
>DroEre_CAF1 9583 119 + 1
UCCUGUCUC-CAGUAUCCUGUCCCGCUGCUGUCCUGUUCUCCUGGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCA
..(((....-)))..............(((((((((((.((..(((..((((.((..((.......))..))))))....)))....((((((.....)))))))).)))))).))))). ( -38.80)
>DroYak_CAF1 6908 120 + 1
UCCUGUCUCCCAGUAUCCUGUCGCGAUGCUGUCCUGUUCUCCUGGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAAGGGCA
....((((..((((((((....).)))))))(((((((.((..(((..((((.((..((.......))..))))))....)))....((((((.....)))))))).))))))).)))). ( -42.30)
>consensus
UCCUGUCUU_CUGUAUCCUGUCCCGGUGCUGUCCUGUUCUCCUGGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCA
...........................(((((((((((.((..(((..((((.((..((.......))..))))))....)))....((((((.....)))))))).)))))).))))). (-36.28 = -36.68 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	7,196,041 – 7,196,148
Length	107
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	92.93
Mean single sequence MFE	-40.80
Consensus MFE	-35.02
Energy contribution	-35.42
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.86
SVM decision value	1.15
SVM RNA-class probability	0.922595
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7196041 107 + 23771897
CCUAGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCACACCAAAUGGCUCAGACACCAUGGGUG----------
.....(((((((((.....)))))))))((((((((...((....((((((((.....))))))))...))..))))))))(((..((((........)))).))).---------- ( -37.30)
>DroSec_CAF1 9620 107 + 1
CCUGGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCACACCAAAUGGCUCAGACACCAUGGCUG----------
((((((((((((((.....)))))))))((((((((...((....((((((((.....))))))))...))..)))))))).))).((((........))))))...---------- ( -36.70)
>DroSim_CAF1 1540 117 + 1
CCUGGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCACACCAAAUGGCUCAGACACCAUGGGUGUGGCGACUAA
((((.(((((((((.....))))))))).((((((.....)).....((((((.....)))))))))).))))..((.((((((..((((........)))).)))))).))..... ( -44.80)
>DroEre_CAF1 9622 117 + 1
CCUGGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCACACCAAAUGGCUCAGACACCAUGGGUGUGGCAGCUAA
..((((((((((((.....)))))))))((((((((...((....((((((((.....))))))))...))..)))))))).)))..((((((..(((((...))))).).))))). ( -44.20)
>DroYak_CAF1 6948 117 + 1
CCUGGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAAGGGCACACCAAAUGGCUCAGACACCAUGGGUGUGGUGAUUGA
.(((((((((((((.....))))))).(((((.(((.....(((.((((((((.....))))))))....)))...))))))))....))).))).((((((....))))))..... ( -41.00)
>consensus
CCUGGCUGGGCGGACGUCUUCUGUUUAGGUGUCGUUAAAUGCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCACACCAAAUGGCUCAGACACCAUGGGUGUGG____U_A
((((((((((((((.....)))))))))((((((((...((....((((((((.....))))))))...))..)))))))).))).((((........))))))............. (-35.02 = -35.42 +   0.40)

alignment

secondary structure

dotplot

Window 6

Location	7,196,081 – 7,196,176
Length	95
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	85.52
Mean single sequence MFE	-28.04
Consensus MFE	-20.84
Energy contribution	-22.16
Covariance contribution	1.32
Combinations/Pair	1.05
Mean z-score	-2.22
Structure conservation index	0.74
SVM decision value	1.05
SVM RNA-class probability	0.906180
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7196081 95 + 23771897
GCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCACACCAAAUGGCUCAGACACCAUGGGUG---------------UGAUUAUUCAAAUAUUUAAACAAAAUCA
.....((((((((.....))))))))......(((..(((((((..((((........)))).))))---------------)).)..)))................... ( -26.10)
>DroSec_CAF1 9660 95 + 1
GCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCACACCAAAUGGCUCAGACACCAUGGCUG---------------UGGUUAUUAAAAUAUUUAAACAAAAGCA
.(((.((((((((.....))))))))....))).....(((((((..(((........)))))).))---------------)).......................... ( -21.30)
>DroSim_CAF1 1580 110 + 1
GCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCACACCAAAUGGCUCAGACACCAUGGGUGUGGCGACUAAAAGUGUGGUUAUUCAAAUAUUUAAACAAAAACA
.(((.((((((((.....))))))))....)))..((.((((((..((((........)))).)))))).)).....((((((..........))))))........... ( -30.70)
>DroEre_CAF1 9662 109 + 1
GCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCACACCAAAUGGCUCAGACACCAUGGGUGUGGCAGCUAAAAGUUUUG-UAUCAAAAUAUUAAAACAAAAUCC
.....((((((((.....)))))))).....(((..(.((((((..((((........)))).)))))).)........((((((-(((....))).))))))....))) ( -30.50)
>DroYak_CAF1 6988 109 + 1
GCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAAGGGCACACCAAAUGGCUCAGACACCAUGGGUGUGGUGAUUGAAAGUUUUG-UAUUCAAAUAUUAAAACAAAAGCU
(((((((((((((.....))))))..(....)))))))).........(((((((.((((((....)))))).))))..((((((-(((....))).))))))....))) ( -31.60)
>consensus
GCCUUUUGCCAACAAGUCGUUGGCGACAACAGGAACGGCACACCAAAUGGCUCAGACACCAUGGGUGUGG____U_AAAGU_UGGUUAUUCAAAUAUUUAAACAAAAGCA
.(((.((((((((.....))))))))....)))...(.((((((..((((........)))).)))))).)....................................... (-20.84 = -22.16 +   1.32)

alignment

secondary structure

dotplot

Window 7

Location	7,196,081 – 7,196,176
Length	95
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	85.52
Mean single sequence MFE	-28.90
Consensus MFE	-19.92
Energy contribution	-21.24
Covariance contribution	1.32
Combinations/Pair	1.04
Mean z-score	-1.77
Structure conservation index	0.69
SVM decision value	0.11
SVM RNA-class probability	0.588485
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7196081 95 - 23771897
UGAUUUUGUUUAAAUAUUUGAAUAAUCA---------------CACCCAUGGUGUCUGAGCCAUUUGGUGUGCCGUUCCUGUUGUCGCCAACGACUUGUUGGCAAAAGGC
.(((.((((((((....)))))))).((---------------((((.(((((......)))))..))))))...........)))((((((.....))))))....... ( -26.30)
>DroSec_CAF1 9660 95 - 1
UGCUUUUGUUUAAAUAUUUUAAUAACCA---------------CAGCCAUGGUGUCUGAGCCAUUUGGUGUGCCGUUCCUGUUGUCGCCAACGACUUGUUGGCAAAAGGC
.((((((.................((.(---------------(((..((((..(....(((....))))..))))..)))).)).((((((.....)))))).)))))) ( -25.70)
>DroSim_CAF1 1580 110 - 1
UGUUUUUGUUUAAAUAUUUGAAUAACCACACUUUUAGUCGCCACACCCAUGGUGUCUGAGCCAUUUGGUGUGCCGUUCCUGUUGUCGCCAACGACUUGUUGGCAAAAGGC
(((..((((((((....))))))))..)))(((((...((.((((((.(((((......)))))..)))))).))...........((((((.....))))))))))).. ( -31.80)
>DroEre_CAF1 9662 109 - 1
GGAUUUUGUUUUAAUAUUUUGAUA-CAAAACUUUUAGCUGCCACACCCAUGGUGUCUGAGCCAUUUGGUGUGCCGUUCCUGUUGUCGCCAACGACUUGUUGGCAAAAGGC
...((((((.((((....)))).)-)))))((((((((.((.(((((.(((((......)))))..))))))).))).........((((((.....))))))))))).. ( -31.80)
>DroYak_CAF1 6988 109 - 1
AGCUUUUGUUUUAAUAUUUGAAUA-CAAAACUUUCAAUCACCACACCCAUGGUGUCUGAGCCAUUUGGUGUGCCCUUCCUGUUGUCGCCAACGACUUGUUGGCAAAAGGC
.((((((....(((((.(((((..-.......)))))....((((((.(((((......)))))..)))))).......)))))..((((((.....)))))).)))))) ( -28.90)
>consensus
UGAUUUUGUUUAAAUAUUUGAAUAACCA_ACUUU_A____CCACACCCAUGGUGUCUGAGCCAUUUGGUGUGCCGUUCCUGUUGUCGCCAACGACUUGUUGGCAAAAGGC
.((((((..................................((((((.(((((......)))))..))))))..............((((((.....)))))).)))))) (-19.92 = -21.24 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:30 2006