Locus 1745

Sequence ID	3L_DroMel_CAF1
Location	5,041,769 – 5,041,960
Length	191
Max. P	0.998600

overview

Window 1

Location	5,041,769 – 5,041,889
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.25
Mean single sequence MFE	-27.24
Consensus MFE	-25.64
Energy contribution	-26.04
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.94
SVM decision value	1.00
SVM RNA-class probability	0.898184
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5041769 120 - 23771897
AUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAAGCAAAGCUUCUUUAAAGCCAAAAAUAAACUAAUGUGAACGU
..(((((((((((((((((((...(((......)))..((....)).......))))))))))))).....((......))..)))))).....................(((....))) ( -27.70)
>DroSec_CAF1 248263 120 - 1
AUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAAGCAAAGCUUCUUCAAAGCCAAAAAUAAACUAAUGUGGAUGU
..(((((((((((((((((((...(((......)))..((....)).......))))))))))))).....((......))..)))))).......(((...((......)).))).... ( -28.30)
>DroSim_CAF1 269124 120 - 1
AUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAAGCAAAGCUUCUUUAAAGCCAAAAAUAAACUAGUGUGGAUGU
..(((((((((((((((((((...(((......)))..((....)).......))))))))))))).....((......))..)))))).......(((...((......)).))).... ( -28.60)
>DroEre_CAF1 251702 120 - 1
AUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAAGCAAAGCUCCUUAAAAGCCAAAAAUAAACUAAUGUGCAUGU
......((((((............(((......))).(((((.(((.......((((.((....)).))))((......))..))))))))...)))))).................... ( -25.00)
>DroYak_CAF1 258066 120 - 1
AUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAUGCAAAGCUCCUUUAAAGCCAAAAAUAAACUAAUGUGCAUGU
......((((((............(((......)))((((((.(((.......((((.((....)).))))(((....)))..)))))))))..)))))).................... ( -26.60)
>consensus
AUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAAGCAAAGCUUCUUUAAAGCCAAAAAUAAACUAAUGUGCAUGU
..(((((((((((((((((((...(((......)))..((....)).......))))))))))))).....((......))..))))))............................... (-25.64 = -26.04 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	5,041,809 – 5,041,929
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.67
Mean single sequence MFE	-32.70
Consensus MFE	-32.70
Energy contribution	-32.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	1.00
SVM decision value	1.66
SVM RNA-class probability	0.970283
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5041809 120 - 23771897
CCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAAG
....(((((..((.((((.((((.....))))..)))).))..)))))(((((((((((((...(((......)))..((....)).......))))))))))))).............. ( -32.70)
>DroSec_CAF1 248303 120 - 1
CCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAAG
....(((((..((.((((.((((.....))))..)))).))..)))))(((((((((((((...(((......)))..((....)).......))))))))))))).............. ( -32.70)
>DroSim_CAF1 269164 120 - 1
CCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAAG
....(((((..((.((((.((((.....))))..)))).))..)))))(((((((((((((...(((......)))..((....)).......))))))))))))).............. ( -32.70)
>DroEre_CAF1 251742 120 - 1
CCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAAG
....(((((..((.((((.((((.....))))..)))).))..)))))(((((((((((((...(((......)))..((....)).......))))))))))))).............. ( -32.70)
>DroYak_CAF1 258106 120 - 1
CCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAUG
....(((((..((.((((.((((.....))))..)))).))..)))))(((((((((((((...(((......)))..((....)).......))))))))))))).............. ( -32.70)
>consensus
CCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAGGGCGCUAAAACAAUUUACGGUUAGCCAUAAAGCAAUUAAG
....(((((..((.((((.((((.....))))..)))).))..)))))(((((((((((((...(((......)))..((....)).......))))))))))))).............. (-32.70 = -32.70 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	5,041,849 – 5,041,960
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.86
Mean single sequence MFE	-23.70
Consensus MFE	-23.26
Energy contribution	-23.26
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.28
Structure conservation index	0.98
SVM decision value	0.92
SVM RNA-class probability	0.881702
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5041849 111 + 23771897
CUUUGCCCAUAUCGGCGGUUCCACAAUUAGCCAACUUCAUUAUGCCUGCUGCUAAUUGCAAUAACAAAACAAAGUCUAGGCAAAUGUGUAAGCCAUAAAUGAUAACCGGCA---------
...((((..(((((((((((........)))).((..((((.((((((.(((.....)))...((........)).)))))))))).))..)))......))))...))))--------- ( -23.10)
>DroSec_CAF1 248343 111 + 1
CUUUGCCCAUAUCGGCGGUUCCACAAUUAGCCAACUUCAUUAUGCCUGCUGCUAAUUGCAAUAACAAAACAAAGUCUAGGCAAAUGUGUAAGCCAUAAAUGAUAACCGGCA---------
...((((..(((((((((((........)))).((..((((.((((((.(((.....)))...((........)).)))))))))).))..)))......))))...))))--------- ( -23.10)
>DroSim_CAF1 269204 111 + 1
CUUUGCCCAUAUCGGCGGUUCCACAAUUAGCCAACUUCAUUAUGCCUGCUGCUAAUUGCAAUAACAAAACAAAGUCUAGGCAAAUGUGUAAGCCAUAAAUGAUAACCGGCA---------
...((((..(((((((((((........)))).((..((((.((((((.(((.....)))...((........)).)))))))))).))..)))......))))...))))--------- ( -23.10)
>DroEre_CAF1 251782 111 + 1
CUUUGCCCAUAUCGGCGGUUCCACAAUUAGCCAACUUCAUUAUGCCUGCUGCUAAUUGCAAUAACAAAACAAAGUCUAGGCAAAUGUGUAAGCCAUAAAUGAUAACCGGCA---------
...((((..(((((((((((........)))).((..((((.((((((.(((.....)))...((........)).)))))))))).))..)))......))))...))))--------- ( -23.10)
>DroYak_CAF1 258146 120 + 1
CUUUGCCCAUAUCGGCGGUUCCACAAUUAGCCAACUUCAUUAUGCCUGCUGCUAAUUGCAAUAACAAAACAAAGUCUAGGCAAAUGUGUAAGCCAUAAAUGAUAACCGGCAACUGGCAAC
..(((((......(((((((........)))).((..((((.((((((.(((.....)))...((........)).)))))))))).))..))).............(....).))))). ( -26.10)
>consensus
CUUUGCCCAUAUCGGCGGUUCCACAAUUAGCCAACUUCAUUAUGCCUGCUGCUAAUUGCAAUAACAAAACAAAGUCUAGGCAAAUGUGUAAGCCAUAAAUGAUAACCGGCA_________
...((((..(((((((((((........)))).((..((((.((((((.(((.....)))...((........)).)))))))))).))..)))......))))...))))......... (-23.26 = -23.26 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	5,041,849 – 5,041,960
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.86
Mean single sequence MFE	-33.38
Consensus MFE	-32.34
Energy contribution	-32.34
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.98
Structure conservation index	0.97
SVM decision value	3.16
SVM RNA-class probability	0.998600
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5041849 111 - 23771897
---------UGCCGGUUAUCAUUUAUGGCUUACACAUUUGCCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAG
---------((((.((.(((......(((...((((.(((((..(((((..((.((((.((((.....))))..)))).))..)))))))).)).)))).....)))))))).))))... ( -32.30)
>DroSec_CAF1 248343 111 - 1
---------UGCCGGUUAUCAUUUAUGGCUUACACAUUUGCCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAG
---------((((.((.(((......(((...((((.(((((..(((((..((.((((.((((.....))))..)))).))..)))))))).)).)))).....)))))))).))))... ( -32.30)
>DroSim_CAF1 269204 111 - 1
---------UGCCGGUUAUCAUUUAUGGCUUACACAUUUGCCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAG
---------((((.((.(((......(((...((((.(((((..(((((..((.((((.((((.....))))..)))).))..)))))))).)).)))).....)))))))).))))... ( -32.30)
>DroEre_CAF1 251782 111 - 1
---------UGCCGGUUAUCAUUUAUGGCUUACACAUUUGCCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAG
---------((((.((.(((......(((...((((.(((((..(((((..((.((((.((((.....))))..)))).))..)))))))).)).)))).....)))))))).))))... ( -32.30)
>DroYak_CAF1 258146 120 - 1
GUUGCCAGUUGCCGGUUAUCAUUUAUGGCUUACACAUUUGCCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAG
.(((((.((((.(((((.((((...(((((.((.(((((((((.(((........))).((((.....)))).))))).))))..)).)))))...))))))))).))))...))))).. ( -37.70)
>consensus
_________UGCCGGUUAUCAUUUAUGGCUUACACAUUUGCCUAGACUUUGUUUUGUUAUUGCAAUUAGCAGCAGGCAUAAUGAAGUUGGCUAAUUGUGGAACCGCCGAUAUGGGCAAAG
.........((((.((.(((......(((...((((.(((((..(((((..((.((((.((((.....))))..)))).))..)))))))).)).)))).....)))))))).))))... (-32.34 = -32.34 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:09 2006