Locus 7991

Sequence ID	X_DroMel_CAF1
Location	19,884,020 – 19,884,214
Length	194
Max. P	0.987926

overview

Window 7

Location	19,884,020 – 19,884,135
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.41
Mean single sequence MFE	-34.24
Consensus MFE	-30.52
Energy contribution	-30.52
Covariance contribution	-0.00
Combinations/Pair	1.08
Mean z-score	-2.12
Structure conservation index	0.89
SVM decision value	1.95
SVM RNA-class probability	0.983712
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19884020 115 + 22224390
CGAGUCCAUUGUACGUGCUUCGUUGGCGGGACUGCGGGAAUCAAACCAGAAACCAGAAAACCAAACUUUCAAUGGACUG---GCUGGCAGCAAGUCAAGCUGCCCAAAAACGGAAAAC--
(.(((((((((...(((((.....)))((.......((..((......))..))......))..))...))))))))).---)..((((((.......))))))..............-- ( -31.42)
>DroSec_CAF1 37742 113 + 1
AGAGUCCAUUGUACGUGCUUCGUUGGCGGAGCUGCGGGAACC--ACCAGAAACCAGAAAACAAAACUUUCAAUGGACUG---GCUGGCAGCAAGUCAAGCUGCCCGAAAACAGAAAAC--
..(((((((((..(((((((((....)))))).)))((....--.))......................))))))))).---.(.((((((.......)))))).)............-- ( -35.80)
>DroSim_CAF1 28477 113 + 1
CGAGUCCAUUGUACGUGCUUCGUUGGCGGAGCUGCGGGAACC--ACCAGAAACCAGAAAACAAAACUUUCAAUGGACUG---GCUGGCAGCAAGUCAAGCUGCCCGAAAACAGAAAAC--
(.(((((((((..(((((((((....)))))).)))((....--.))......................))))))))).---)(.((((((.......)))))).)............-- ( -36.60)
>DroEre_CAF1 17547 103 + 1
CAAGUCCAUUGUACGUGCUUCGUUGGCGGGACGGAGG------------AACCCAGAAAACAAAACUUUCAAUGGACUG---GCUGGCAGCAAGUCAAGCUGCCCAAAAUCAGAAAAC--
..(((((((((...(((((.....)))(((.......------------..)))..........))...))))))))).---...((((((.......))))))..............-- ( -29.90)
>DroYak_CAF1 14235 108 + 1
CGAGUCCAUUGUACGUGCUCCGUUGGCGGGGCUGGGG------------AAUCCAGAAAACAAAACUUUCAAUGGACUGACGGCAGGCAGCAAGUCAAGCUGCCCGAAAUCAGAAAACAA
..(((((((((...((((((((....))))))(((..------------...))).........))...)))))))))((...(.((((((.......)))))).)...))......... ( -37.50)
>consensus
CGAGUCCAUUGUACGUGCUUCGUUGGCGGGGCUGCGGGAA_C__ACCAGAAACCAGAAAACAAAACUUUCAAUGGACUG___GCUGGCAGCAAGUCAAGCUGCCCGAAAACAGAAAAC__
..(((((((((...((((((((....))))))...((...............))..........))...))))))))).......((((((.......))))))................ (-30.52 = -30.52 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	19,884,020 – 19,884,135
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.41
Mean single sequence MFE	-35.58
Consensus MFE	-29.22
Energy contribution	-29.26
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.73
Structure conservation index	0.82
SVM decision value	0.62
SVM RNA-class probability	0.802016
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19884020 115 - 22224390
--GUUUUCCGUUUUUGGGCAGCUUGACUUGCUGCCAGC---CAGUCCAUUGAAAGUUUGGUUUUCUGGUUUCUGGUUUGAUUCCCGCAGUCCCGCCAACGAAGCACGUACAAUGGACUCG
--..............((((((.......))))))...---.(((((((((.......((....)).(((((((((..((((.....))))..))))..))))).....))))))))).. ( -33.10)
>DroSec_CAF1 37742 113 - 1
--GUUUUCUGUUUUCGGGCAGCUUGACUUGCUGCCAGC---CAGUCCAUUGAAAGUUUUGUUUUCUGGUUUCUGGU--GGUUCCCGCAGCUCCGCCAACGAAGCACGUACAAUGGACUCU
--..............((((((.......))))))...---.((((((((((..((((((((...(((...(((.(--((...))))))..)))..))))))))...).))))))))).. ( -36.00)
>DroSim_CAF1 28477 113 - 1
--GUUUUCUGUUUUCGGGCAGCUUGACUUGCUGCCAGC---CAGUCCAUUGAAAGUUUUGUUUUCUGGUUUCUGGU--GGUUCCCGCAGCUCCGCCAACGAAGCACGUACAAUGGACUCG
--..............((((((.......))))))...---.((((((((((..((((((((...(((...(((.(--((...))))))..)))..))))))))...).))))))))).. ( -36.00)
>DroEre_CAF1 17547 103 - 1
--GUUUUCUGAUUUUGGGCAGCUUGACUUGCUGCCAGC---CAGUCCAUUGAAAGUUUUGUUUUCUGGGUU------------CCUCCGUCCCGCCAACGAAGCACGUACAAUGGACUUG
--..............((((((.......))))))...---.((((((((((..((((((((...((((..------------.......))))..))))))))...).))))))))).. ( -34.10)
>DroYak_CAF1 14235 108 - 1
UUGUUUUCUGAUUUCGGGCAGCUUGACUUGCUGCCUGCCGUCAGUCCAUUGAAAGUUUUGUUUUCUGGAUU------------CCCCAGCCCCGCCAACGGAGCACGUACAAUGGACUCG
........((((..((((((((.......))))))))..))))((((((((..............(((...------------..)))((.(((....))).)).....))))))))... ( -38.70)
>consensus
__GUUUUCUGUUUUCGGGCAGCUUGACUUGCUGCCAGC___CAGUCCAUUGAAAGUUUUGUUUUCUGGUUUCUGGU__G_UUCCCGCAGCCCCGCCAACGAAGCACGUACAAUGGACUCG
................((((((.......)))))).......((((((((((..((((((((...(((.......................)))..))))))))...).))))))))).. (-29.22 = -29.26 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	19,884,060 – 19,884,174
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.81
Mean single sequence MFE	-25.96
Consensus MFE	-21.52
Energy contribution	-21.72
Covariance contribution	0.20
Combinations/Pair	1.10
Mean z-score	-2.41
Structure conservation index	0.83
SVM decision value	2.10
SVM RNA-class probability	0.987926
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19884060 114 + 22224390
UCAAACCAGAAACCAGAAAACCAAACUUUCAAUGGACUG---GCUGGCAGCAAGUCAAGCUGCCCAAAAACGGAAAAC---AAAAAAUCCCAAUCGACUGGGGAUGGUAUCCAUCUUUUU
.....((.....((((....(((.........))).)))---)..((((((.......)))))).......)).....---.......((((......))))(((((...)))))..... ( -27.00)
>DroSec_CAF1 37782 112 + 1
CC--ACCAGAAACCAGAAAACAAAACUUUCAAUGGACUG---GCUGGCAGCAAGUCAAGCUGCCCGAAAACAGAAAAC---AAAAAAUUCCAAUCGACUGGGGAUGGUAUCCAUAUUUUU
((--.((((...(((((((.......))))..))).(((---.(.((((((.......)))))).)....))).....---................))))))((((...))))...... ( -26.50)
>DroSim_CAF1 28517 112 + 1
CC--ACCAGAAACCAGAAAACAAAACUUUCAAUGGACUG---GCUGGCAGCAAGUCAAGCUGCCCGAAAACAGAAAAC---AAAAAGUCCCAAUCGACUGGGGAUGGUAUCCAUCUUUUU
..--.((((...(((((((.......))))..))).(((---.(.((((((.......)))))).)....))).....---................))))((((((...)))))).... ( -28.30)
>DroEre_CAF1 17584 105 + 1
---------AACCCAGAAAACAAAACUUUCAAUGGACUG---GCUGGCAGCAAGUCAAGCUGCCCAAAAUCAGAAAAC---AAAAAAUACGAAUUGACUGGGGAUGGUAUCCAACCUUUU
---------..(((((.........((......)).(((---(..((((((.......)))))).....)))).....---................)))))...(((.....))).... ( -23.10)
>DroYak_CAF1 14272 111 + 1
---------AAUCCAGAAAACAAAACUUUCAAUGGACUGACGGCAGGCAGCAAGUCAAGCUGCCCGAAAUCAGAAAACAACAAAAAAUACCAAUUGACUGGGGAUUGUAUCUAUCCUUUU
---------..((((((((.......))))..))))((((...(.((((((.......)))))).)...))))................(((......)))((((.......)))).... ( -24.90)
>consensus
_C__ACCAGAAACCAGAAAACAAAACUUUCAAUGGACUG___GCUGGCAGCAAGUCAAGCUGCCCGAAAACAGAAAAC___AAAAAAUACCAAUCGACUGGGGAUGGUAUCCAUCUUUUU
............((((.........((......)).(((......((((((.......))))))......)))........................))))((((((...)))))).... (-21.52 = -21.72 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	19,884,060 – 19,884,174
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.81
Mean single sequence MFE	-31.34
Consensus MFE	-22.16
Energy contribution	-22.56
Covariance contribution	0.40
Combinations/Pair	1.07
Mean z-score	-2.00
Structure conservation index	0.71
SVM decision value	0.42
SVM RNA-class probability	0.728717
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19884060 114 - 22224390
AAAAAGAUGGAUACCAUCCCCAGUCGAUUGGGAUUUUUU---GUUUUCCGUUUUUGGGCAGCUUGACUUGCUGCCAGC---CAGUCCAUUGAAAGUUUGGUUUUCUGGUUUCUGGUUUGA
..(((((((((...((..(((((....)))))......)---)...))))))))).((((((.......))))))(((---(((.(((..(((((.....))))))))...))))))... ( -35.50)
>DroSec_CAF1 37782 112 - 1
AAAAAUAUGGAUACCAUCCCCAGUCGAUUGGAAUUUUUU---GUUUUCUGUUUUCGGGCAGCUUGACUUGCUGCCAGC---CAGUCCAUUGAAAGUUUUGUUUUCUGGUUUCUGGU--GG
...........(((((...((((..((.(..(((((((.---.....(((......((((((.......))))))...---)))......)))))))..)))..))))....))))--). ( -28.50)
>DroSim_CAF1 28517 112 - 1
AAAAAGAUGGAUACCAUCCCCAGUCGAUUGGGACUUUUU---GUUUUCUGUUUUCGGGCAGCUUGACUUGCUGCCAGC---CAGUCCAUUGAAAGUUUUGUUUUCUGGUUUCUGGU--GG
.....(((((...)))))(((((....))))).......---..............((((((.......)))))).((---(((.(((..(((((.....))))))))...)))))--.. ( -32.60)
>DroEre_CAF1 17584 105 - 1
AAAAGGUUGGAUACCAUCCCCAGUCAAUUCGUAUUUUUU---GUUUUCUGAUUUUGGGCAGCUUGACUUGCUGCCAGC---CAGUCCAUUGAAAGUUUUGUUUUCUGGGUU---------
....(((.....)))...(((((..(((....((((((.---.....(((......((((((.......))))))...---)))......))))))...)))..)))))..--------- ( -27.70)
>DroYak_CAF1 14272 111 - 1
AAAAGGAUAGAUACAAUCCCCAGUCAAUUGGUAUUUUUUGUUGUUUUCUGAUUUCGGGCAGCUUGACUUGCUGCCUGCCGUCAGUCCAUUGAAAGUUUUGUUUUCUGGAUU---------
....((((.......))))((((..(((....((((((...((....(((((..((((((((.......))))))))..)))))..))..))))))...)))..))))...--------- ( -32.40)
>consensus
AAAAAGAUGGAUACCAUCCCCAGUCGAUUGGGAUUUUUU___GUUUUCUGUUUUCGGGCAGCUUGACUUGCUGCCAGC___CAGUCCAUUGAAAGUUUUGUUUUCUGGUUUCUGGU__G_
.....(((((...))))).((((..(((..(.((((((.........(((......((((((.......))))))......)))......)))))))..)))..))))............ (-22.16 = -22.56 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	19,884,099 – 19,884,214
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.63
Mean single sequence MFE	-24.88
Consensus MFE	-18.02
Energy contribution	-18.54
Covariance contribution	0.52
Combinations/Pair	1.09
Mean z-score	-1.84
Structure conservation index	0.72
SVM decision value	0.24
SVM RNA-class probability	0.648490
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19884099 115 + 22224390
--GCUGGCAGCAAGUCAAGCUGCCCAAAAACGGAAAAC---AAAAAAUCCCAAUCGACUGGGGAUGGUAUCCAUCUUUUUAAUCAAAGCCAACUCCCAAUGCAAAAUAUUGCUCUACCCA
--...((((((.......)))))).......(((....---.......((((......))))(((((...)))))..................)))....((((....))))........ ( -25.20)
>DroSec_CAF1 37819 115 + 1
--GCUGGCAGCAAGUCAAGCUGCCCGAAAACAGAAAAC---AAAAAAUUCCAAUCGACUGGGGAUGGUAUCCAUAUUUUUAAUCAAAGCCAACUCGCAAUGCAAAAUAUUGCUCCACCCA
--.(.((((((.......)))))).)............---..................(((..((((...................))))....((((((.....))))))....))). ( -22.61)
>DroSim_CAF1 28554 115 + 1
--GCUGGCAGCAAGUCAAGCUGCCCGAAAACAGAAAAC---AAAAAGUCCCAAUCGACUGGGGAUGGUAUCCAUCUUUUUAAUCAAAGCCAACUCGCAAUGCAAAAUAUUGCUCCACCCA
--.(.((((((.......)))))).)............---....((((......))))((((((((...)))))....................((((((.....))))))....))). ( -27.90)
>DroEre_CAF1 17614 115 + 1
--GCUGGCAGCAAGUCAAGCUGCCCAAAAUCAGAAAAC---AAAAAAUACGAAUUGACUGGGGAUGGUAUCCAACCUUUUAAUCAAAGCCAACUCCCAAUGCAAAAUAUGGUUCCAGCCA
--((.((((((.......))))))..............---.................(((((.((((...................)))).).))))..))......((((....)))) ( -23.81)
>DroYak_CAF1 14303 115 + 1
CGGCAGGCAGCAAGUCAAGCUGCCCGAAAUCAGAAAACAACAAAAAAUACCAAUUGACUGGGGAUUGUAUCUAUCCUUUUAAUCAAAGCCAACUCCCAAUGCAAAAUAUUGUGCU-----
.(((.((((((.......)))))).............................((((..((((((.......))))))....)))).)))..........(((........))).----- ( -24.90)
>consensus
__GCUGGCAGCAAGUCAAGCUGCCCGAAAACAGAAAAC___AAAAAAUACCAAUCGACUGGGGAUGGUAUCCAUCUUUUUAAUCAAAGCCAACUCCCAAUGCAAAAUAUUGCUCCACCCA
..(((((((((.......))))))...............................((..((((((((...))))))))....))..)))...........((((....))))........ (-18.02 = -18.54 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:52:42 2006