Locus 8515

Sequence ID	3L_DroMel_CAF1
Location	22,305,199 – 22,305,473
Length	274
Max. P	0.986426

overview

Window 9

Location	22,305,199 – 22,305,313
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	85.24
Mean single sequence MFE	-37.42
Consensus MFE	-25.26
Energy contribution	-25.30
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-1.98
Structure conservation index	0.68
SVM decision value	0.31
SVM RNA-class probability	0.682232
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22305199 114 + 23771897
AGACGAGUGGCGGGGAGGGGGGUAAGGCUUCAGUUUUGGGGAAUGUAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCU------AUAUGAUGCAUAUGUAUGCCACUCAUUCUUUG
....((((((((((((..((((.....))))..))))(.(..(((((((((((.(((.((....)).)))....)))).)))------))))..).).......))))))))........ ( -39.20)
>DroSec_CAF1 63801 102 + 1
AGGCGAGUGG--GGCAGGGGG---------CAGUU-UGGCCAAUGGAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCU------AUAUGAUGCAUAUGUAUGCCACUCAUUCUUUG
....((((((--(((((((((---------(((((-.(((((.((......))))))).....))))))).)))))))....------.....((((....)))).))))))........ ( -38.30)
>DroSim_CAF1 45840 103 + 1
AGGCGAGUGG--GGCAGGGGG---------CAGUUUUGGGCAAUGGAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCU------AUAUGAUGCAUAUGUAUGCCACUCAUUCUUUG
....((((((--(((((((((---------(((((..((((.(((......))).))).)...))))))).)))))))....------.....((((....)))).))))))........ ( -36.40)
>DroEre_CAF1 62227 102 + 1
AGACGAGUGG--GG----------------CAGUUUUGGGGCUCGGAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCUACUCGUAUAUGAUGCAUAUGUAUGCCACUCAUUCUUUG
..((((((((--((----------------(((((.....((((....))))..)))))))(((((.........)))))))))))))..((((.((((....))))...))))...... ( -34.60)
>DroYak_CAF1 39464 95 + 1
AGACGAGUGG--GG----------------CAGUUUUGCGGAU-GGAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCU------AUAUGAUGCAUAUGUGUGCCACUCAUUCUUUG
....((((((--.(----------------((....((((.((-(((..((((.(((.((....)).)))....)))).)))------))....))))....))).))))))........ ( -38.60)
>consensus
AGACGAGUGG__GG_AGGGGG_________CAGUUUUGGGGAAUGGAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCU______AUAUGAUGCAUAUGUAUGCCACUCAUUCUUUG
....((((((..................................(((..((((.(((.((....)).)))....)))).)))...........((((....)))).))))))........ (-25.26 = -25.30 +   0.04)

alignment

secondary structure

dotplot

Window 0

Location	22,305,199 – 22,305,313
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.24
Mean single sequence MFE	-26.41
Consensus MFE	-20.24
Energy contribution	-20.44
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.41
Structure conservation index	0.77
SVM decision value	1.53
SVM RNA-class probability	0.961925
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22305199 114 - 23771897
CAAAGAAUGAGUGGCAUACAUAUGCAUCAUAU------AGAUGGCAAAAAGGCAGCCACAGCAGCCAUGCCCCUACAUUCCCCAAAACUGAAGCCUUACCCCCCUCCCCGCCACUCGUCU
...(((.((((((((.......((((((....------.))).)))..(((((.......(((....)))............((....))..)))))............))))))))))) ( -27.90)
>DroSec_CAF1 63801 102 - 1
CAAAGAAUGAGUGGCAUACAUAUGCAUCAUAU------AGAUGGCAAAAAGGCAGCCACAGCAGCCAUGCCCCUCCAUUGGCCA-AACUG---------CCCCCUGCC--CCACUCGCCU
........((((((........((((((....------.))).)))....(((((.....((((....(((........)))..-..)))---------)...)))))--)))))).... ( -29.50)
>DroSim_CAF1 45840 103 - 1
CAAAGAAUGAGUGGCAUACAUAUGCAUCAUAU------AGAUGGCAAAAAGGCAGCCACAGCAGCCAUGCCCCUCCAUUGCCCAAAACUG---------CCCCCUGCC--CCACUCGCCU
........(((((((((....)))).......------....((((....(((((........((.(((......))).))......)))---------))...))))--.))))).... ( -24.74)
>DroEre_CAF1 62227 102 - 1
CAAAGAAUGAGUGGCAUACAUAUGCAUCAUAUACGAGUAGAUGGCAAAAAGGCAGCCACAGCAGCCAUGCCCCUCCGAGCCCCAAAACUG----------------CC--CCACUCGUCU
......((((...((((....)))).))))..((((((....((((....(((.((....)).)))..((........))........))----------------))--..)))))).. ( -24.30)
>DroYak_CAF1 39464 95 - 1
CAAAGAAUGAGUGGCACACAUAUGCAUCAUAU------AGAUGGCAAAAAGGCAGCCACAGCAGCCAUGCCCCUCC-AUCCGCAAAACUG----------------CC--CCACUCGUCU
...(((.(((((((..((....((((((....------.)))((((....(((.((....)).))).)))).....-....)))....))----------------..--)))))))))) ( -25.60)
>consensus
CAAAGAAUGAGUGGCAUACAUAUGCAUCAUAU______AGAUGGCAAAAAGGCAGCCACAGCAGCCAUGCCCCUCCAUUCCCCAAAACUG_________CCCCCU_CC__CCACUCGUCU
.......((((((((((....)))).................((((....(((.((....)).))).))))........................................))))))... (-20.24 = -20.44 +   0.20)

alignment

secondary structure

dotplot

Window 1

Location	22,305,239 – 22,305,353
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.07
Mean single sequence MFE	-32.90
Consensus MFE	-30.86
Energy contribution	-30.86
Covariance contribution	-0.00
Combinations/Pair	1.06
Mean z-score	-1.61
Structure conservation index	0.94
SVM decision value	2.04
SVM RNA-class probability	0.986426
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22305239 114 + 23771897
GAAUGUAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCU------AUAUGAUGCAUAUGUAUGCCACUCAUUCUUUGGCUCAUUCUUUUUUGGCUGCUCCGCACGAAACUAAAACUA
...(((.((((((.(((.((....)).))).....((((...------..(((((((....))).((((.........)))))))).......))))))))))..)))............ ( -29.30)
>DroSec_CAF1 63829 114 + 1
CAAUGGAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCU------AUAUGAUGCAUAUGUAUGCCACUCAUUCUUUGGCCCCUUCUUUUUUGGCUGCUCCGCACGAAACUAAAACUA
....((((((((..(..((..((((((((.....(((.(((.------....))))))...))).))))).))..)....))))))))..(((((((......)).)))))......... ( -35.50)
>DroSim_CAF1 45869 114 + 1
CAAUGGAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCU------AUAUGAUGCAUAUGUAUGCCACUCAUUCUUUGGCCCCUUCUUUUUUGGCUGCUCCGCACGAAACUAAAACUA
....((((((((..(..((..((((((((.....(((.(((.------....))))))...))).))))).))..)....))))))))..(((((((......)).)))))......... ( -35.50)
>DroEre_CAF1 62249 120 + 1
GCUCGGAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCUACUCGUAUAUGAUGCAUAUGUAUGCCACUCAUUCUUUGGCUCCUUCUUUUUUGGCUGCUCCGCACGAAACUAAAACUA
....((((((((..(..((..((((((((.....(((.(((...........))))))...))).))))).))..)....))))))))..(((((((......)).)))))......... ( -31.80)
>DroYak_CAF1 39486 113 + 1
GAU-GGAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCU------AUAUGAUGCAUAUGUGUGCCACUCAUUCUUUGGCUCCUUCUUUUUUGGCUUCUCCGCACGAAACUAAAACUA
(.(-((((((((..(((.((....)).))).....((((...------..((((.((((....))))...))))....)))).............))))))))))............... ( -32.40)
>consensus
GAAUGGAGGGGCAUGGCUGCUGUGGCUGCCUUUUUGCCAUCU______AUAUGAUGCAUAUGUAUGCCACUCAUUCUUUGGCUCCUUCUUUUUUGGCUGCUCCGCACGAAACUAAAACUA
....((((((((..(..((..((((((((.....(((.(((...........))))))...))).))))).))..)....))))))))..(((((((......)).)))))......... (-30.86 = -30.86 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	22,305,313 – 22,305,433
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.82
Mean single sequence MFE	-30.00
Consensus MFE	-26.02
Energy contribution	-26.62
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.64
Structure conservation index	0.87
SVM decision value	0.94
SVM RNA-class probability	0.886049
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22305313 120 + 23771897
GCUCAUUCUUUUUUGGCUGCUCCGCACGAAACUAAAACUAAUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGCCAUCCAGCGUUUGCUCAUUUUUAGCGCAGGAACCU
((.((........)))).(((((((((((((...((((.....(((.............)))...))))..))))))))).))))..(((.(((((...........))))).))).... ( -29.92)
>DroSec_CAF1 63903 120 + 1
GCCCCUUCUUUUUUGGCUGCUCCGCACGAAACUAAAACUAAUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGCCAUCCAGCGUUUGCUCAUUUUUAGCGCAGGAACCU
(((...........))).(((((((((((((...((((.....(((.............)))...))))..))))))))).))))..(((.(((((...........))))).))).... ( -30.32)
>DroSim_CAF1 45943 120 + 1
GCCCCUUCUUUUUUGGCUGCUCCGCACGAAACUAAAACUAAUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGCCAUCCAGCGUUUGCUCAUUUUUAGCGCAGGAACCU
(((...........))).(((((((((((((...((((.....(((.............)))...))))..))))))))).))))..(((.(((((...........))))).))).... ( -30.32)
>DroEre_CAF1 62329 116 + 1
GCUCCUUCUUUUUUGGCUGCUCCGCACGAAACUAAAACUAAUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGC----CAGCGUUUGCUCAUUUUUAGCGCAGGAACCU
..((((.(.......((((((((((((((((...((((.....(((.............)))...))))..))))))))).))).----))))....(((.......)))).)))).... ( -29.92)
>DroYak_CAF1 39559 116 + 1
GCUCCUUCUUUUUUGGCUUCUCCGCACGAAACUAAAACUAAUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGC----CAGCGUUUGCUCAUUUUUAGCGCAGGAACCU
..((((.......((((((...(((((((((...((((.....(((.............)))...))))..))))))))).))))----))(((((...........))))))))).... ( -29.52)
>consensus
GCUCCUUCUUUUUUGGCUGCUCCGCACGAAACUAAAACUAAUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGCCAUCCAGCGUUUGCUCAUUUUUAGCGCAGGAACCU
.....(((((...(((..(((((((((((((...((((.....(((.............)))...))))..))))))))).))))...)))(((((...........))))))))))... (-26.02 = -26.62 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	22,305,353 – 22,305,473
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.66
Mean single sequence MFE	-29.82
Consensus MFE	-29.08
Energy contribution	-29.08
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.35
Structure conservation index	0.98
SVM decision value	0.95
SVM RNA-class probability	0.888388
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22305353 120 + 23771897
AUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGCCAUCCAGCGUUUGCUCAUUUUUAGCGCAGGAACCUUUUUGUGCCAUUUUAUUUACAGGCAUGUAAACACAGGAGA
...........(((.((.....(((((((((...(((.(((((((.(........).)))).......((((((((....))))))))..........))).))).)))))))))))))) ( -30.20)
>DroSec_CAF1 63943 120 + 1
AUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGCCAUCCAGCGUUUGCUCAUUUUUAGCGCAGGAACCUUUUUGUGCCAUUUUAUUUACAGGCAUGUAAACACACGAGA
...(((.............)))(((((((((...(((.(((((((.(........).)))).......((((((((....))))))))..........))).))).)))))))))..... ( -29.32)
>DroSim_CAF1 45983 120 + 1
AUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGCCAUCCAGCGUUUGCUCAUUUUUAGCGCAGGAACCUUUUUGUGCCAUUUUAUUUACAGGCAUGUAAACACACGAGA
...(((.............)))(((((((((...(((.(((((((.(........).)))).......((((((((....))))))))..........))).))).)))))))))..... ( -29.32)
>DroEre_CAF1 62369 116 + 1
AUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGC----CAGCGUUUGCUCAUUUUUAGCGCAGGAACCUUUUUGUGCCAUUUUAUUUACAGGCAUGUAAACACACGAGA
...(((.............)))(((((((((...(((.(((((((----........)))).......((((((((....))))))))..........))).))).)))))))))..... ( -30.12)
>DroYak_CAF1 39599 116 + 1
AUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGC----CAGCGUUUGCUCAUUUUUAGCGCAGGAACCUUUUUGUGCCAUUUUAUUUACAGGCAUGUAAACACACGAGA
...(((.............)))(((((((((...(((.(((((((----........)))).......((((((((....))))))))..........))).))).)))))))))..... ( -30.12)
>consensus
AUUUGCAAAAAUCUACCACGCAUGUGUUUGCUUUUGUGUGUGAGCCAUCCAGCGUUUGCUCAUUUUUAGCGCAGGAACCUUUUUGUGCCAUUUUAUUUACAGGCAUGUAAACACACGAGA
...(((.............)))(((((((((...(((.((((((......(((....)))........((((((((....)))))))).......)))))).))).)))))))))..... (-29.08 = -29.08 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:41 2006