Locus 1115

Sequence ID	3L_DroMel_CAF1
Location	3,270,141 – 3,270,361
Length	220
Max. P	0.996401

overview

Window 7

Location	3,270,141 – 3,270,241
Length	100
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	74.00
Mean single sequence MFE	-19.25
Consensus MFE	-7.30
Energy contribution	-7.80
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.47
Structure conservation index	0.38
SVM decision value	1.39
SVM RNA-class probability	0.949090
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3270141 100 + 23771897
UAUAGACAGAGUUUUUCCCACAUAUGUGGGCAAAUAAAAAUCCCA--------GCAAUGAAAAGCUGGCAUUUUCACCAACCUCCAAGCUAAACUCGAAGUUUAAACA
..(((((.((((((..(((((....)))))......(((((.(((--------((........))))).)))))................))))))...))))).... ( -25.10)
>DroSec_CAF1 294 99 + 1
UAUAGACAGAGUU-UUCCCACAUAUGUGGGCAAAUAAAAUUCCCA--------GCAAUGAAAAGCUAGCAUUUUCACUAACCUCCAAGCUAAACUCGAAAUUCAAACU
........(((((-(.(((((....)))))...............--------....((((((.......))))))..............))))))............ ( -15.90)
>DroSim_CAF1 319 99 + 1
UAUAGACAGAGUU-UUCCCACAUAUGUGGGCAAAUAAAAUUCCCA--------GCUAUGAAAAGCUAGCAUUUUCACCAACCUUCAAGCUAAACUCGAAAUUGAAACU
........(((((-(.(((((....)))))..............(--------(((.((((.....................))))))))))))))............ ( -17.00)
>DroEre_CAF1 321 88 + 1
-----------UU-GUCCCACAUAUGUGGGCAAAUAAAAUUCCCA--------GCAAUGAAAAGCUGGCAUUUUCACCAACCUCCGAGCUAAACUCGAAGUUCAAACC
-----------((-(.(((((....))))))))..(((((..(((--------((........))))).)))))...........(((((........)))))..... ( -22.20)
>DroYak_CAF1 364 88 + 1
-----------UU-UUCCCACACAUGUGCGCAUAUAAAAAUCUCA--------GCAAUGAAAAGCUGGCAUUUUCACCAACCUCCCAGCUAAACUCCAAGUUCAAACA
-----------..-..........((.((.............(((--------....)))..((((((................)))))).........)).)).... ( -10.49)
>DroAna_CAF1 234 102 + 1
UCUAGAAAAGCUU-UUCGCACACAUGUGAGAA-----AAAUGCUAUCUCUUGUGAAAAGAAAACCUUUUGUUUUCACUAACCUUUGGGCCAAGUUCAAAGAGUUACUU
...(((..(((((-(((.(((....))).)))-----))..)))...))).(((((((.(((....))).)))))))((((((((((((...)))))))).))))... ( -24.80)
>consensus
UAUAGACAGAGUU_UUCCCACAUAUGUGGGCAAAUAAAAAUCCCA________GCAAUGAAAAGCUGGCAUUUUCACCAACCUCCAAGCUAAACUCGAAGUUCAAACU
................(((((....)))))...........................((((((.......))))))................................ ( -7.30 =  -7.80 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	3,270,141 – 3,270,241
Length	100
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	74.00
Mean single sequence MFE	-27.87
Consensus MFE	-16.66
Energy contribution	-16.92
Covariance contribution	0.25
Combinations/Pair	1.39
Mean z-score	-2.79
Structure conservation index	0.60
SVM decision value	2.69
SVM RNA-class probability	0.996401
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3270141 100 - 23771897
UGUUUAAACUUCGAGUUUAGCUUGGAGGUUGGUGAAAAUGCCAGCUUUUCAUUGC--------UGGGAUUUUUAUUUGCCCACAUAUGUGGGAAAAACUCUGUCUAUA
.((((...(((((((.....)))))))...(((((((((.(((((........))--------))).)))))))))..(((((....)))))..)))).......... ( -33.30)
>DroSec_CAF1 294 99 - 1
AGUUUGAAUUUCGAGUUUAGCUUGGAGGUUAGUGAAAAUGCUAGCUUUUCAUUGC--------UGGGAAUUUUAUUUGCCCACAUAUGUGGGAA-AACUCUGUCUAUA
((((((((((((.(((.......((((((((((......))))))))))....))--------).)))))))......(((((....))))).)-))))......... ( -26.40)
>DroSim_CAF1 319 99 - 1
AGUUUCAAUUUCGAGUUUAGCUUGAAGGUUGGUGAAAAUGCUAGCUUUUCAUAGC--------UGGGAAUUUUAUUUGCCCACAUAUGUGGGAA-AACUCUGUCUAUA
............((((((((((.((((((((((......))))))))))...)))--------)..............(((((....))))).)-)))))........ ( -27.80)
>DroEre_CAF1 321 88 - 1
GGUUUGAACUUCGAGUUUAGCUCGGAGGUUGGUGAAAAUGCCAGCUUUUCAUUGC--------UGGGAAUUUUAUUUGCCCACAUAUGUGGGAC-AA-----------
........(((((((.....)))))))...(((((((.(.(((((........))--------))).).)))))))(((((((....))))).)-).----------- ( -31.90)
>DroYak_CAF1 364 88 - 1
UGUUUGAACUUGGAGUUUAGCUGGGAGGUUGGUGAAAAUGCCAGCUUUUCAUUGC--------UGAGAUUUUUAUAUGCGCACAUGUGUGGGAA-AA-----------
...............((((((((..((((((((......))))))))..))..))--------)))).(((((...(((((....))))).)))-))----------- ( -24.40)
>DroAna_CAF1 234 102 - 1
AAGUAACUCUUUGAACUUGGCCCAAAGGUUAGUGAAAACAAAAGGUUUUCUUUUCACAAGAGAUAGCAUUU-----UUCUCACAUGUGUGCGAA-AAGCUUUUCUAGA
...((((.(((((.........)))))))))(((((((.(((....))).))))))).(((((.(((..((-----(((.(((....))).)))-))))))))))... ( -23.40)
>consensus
AGUUUGAACUUCGAGUUUAGCUUGGAGGUUGGUGAAAAUGCCAGCUUUUCAUUGC________UGGGAAUUUUAUUUGCCCACAUAUGUGGGAA_AACUCUGUCUAUA
........(((((((.....)))))))((((((......)))))).................................(((((....)))))................ (-16.66 = -16.92 +   0.25)

alignment

secondary structure

dotplot

Window 9

Location	3,270,172 – 3,270,269
Length	97
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	77.19
Mean single sequence MFE	-25.35
Consensus MFE	-14.62
Energy contribution	-14.32
Covariance contribution	-0.30
Combinations/Pair	1.50
Mean z-score	-2.16
Structure conservation index	0.58
SVM decision value	1.26
SVM RNA-class probability	0.937898
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3270172 97 - 23771897
UUUUCCUAGAGUCUCACCCACGAAUAGUUGUUUAAACUUCGAGUUUAGCUUGGAGGUUGGUGAAAAUGCCAGCUUUUCAUUGC--------UGGGAUUUUUAUUU
.......(((((((((((.((((((....))))...(((((((.....))))))))).))))).....(((((........))--------)))))))))..... ( -27.20)
>DroSec_CAF1 324 97 - 1
UUUUCCUAGAGUCUCAGCCACGAAUUGUAGUUUGAAUUUCGAGUUUAGCUUGGAGGUUAGUGAAAAUGCUAGCUUUUCAUUGC--------UGGGAAUUUUAUUU
..(((((((......((((.(((((....)))))...((((((.....))))))))))((((((((.(....))))))))).)--------))))))........ ( -24.00)
>DroSim_CAF1 349 97 - 1
UUUUCCUAGAGUCUCACCCACGAAUUGUAGUUUCAAUUUCGAGUUUAGCUUGAAGGUUGGUGAAAAUGCUAGCUUUUCAUAGC--------UGGGAAUUUUAUUU
..((((((.....(((((.(((((.......)))..(((((((.....))))))))).)))))....((((........))))--------))))))........ ( -24.30)
>DroEre_CAF1 340 97 - 1
CUUUCCUAGAGUCUCACCCACGAAUAGUGGUUUGAACUUCGAGUUUAGCUCGGAGGUUGGUGAAAAUGCCAGCUUUUCAUUGC--------UGGGAAUUUUAUUU
..(((((((........((((.....))))..(((((((((((.....)))))))((((((......))))))..))))...)--------))))))........ ( -32.90)
>DroYak_CAF1 383 97 - 1
UUUUCUUAGAGUCUCACCCACAAAUAGUUGUUUGAACUUGGAGUUUAGCUGGGAGGUUGGUGAAAAUGCCAGCUUUUCAUUGC--------UGAGAUUUUUAUAU
.......((((((((((((((((((....)))))....))).))..(((((..((((((((......))))))))..))..))--------)))))))))..... ( -28.00)
>DroAna_CAF1 264 100 - 1
UUUGGCCAAUUUCCCACCCUCAAGUAACAAGUAACUCUUUGAACUUGGCCCAAAGGUUAGUGAAAACAAAAGGUUUUCUUUUCACAAGAGAUAGCAUUU-----U
..(((........)))..................(((((((((.((((((....)))))).((((((.....))))))..)))).))))).........-----. ( -15.70)
>consensus
UUUUCCUAGAGUCUCACCCACGAAUAGUAGUUUGAACUUCGAGUUUAGCUUGGAGGUUGGUGAAAAUGCCAGCUUUUCAUUGC________UGGGAAUUUUAUUU
...(((((............................(((((((.....)))))))((((((......))))))..................)))))......... (-14.62 = -14.32 +  -0.30)

alignment

secondary structure

dotplot

Window 0

Location	3,270,241 – 3,270,332
Length	91
Sequences	6
Columns	91
Reading direction	reverse
Mean pairwise identity	79.69
Mean single sequence MFE	-17.36
Consensus MFE	-14.51
Energy contribution	-14.46
Covariance contribution	-0.05
Combinations/Pair	1.26
Mean z-score	-1.65
Structure conservation index	0.84
SVM decision value	0.89
SVM RNA-class probability	0.875666
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3270241 91 - 23771897
CUCCUCCAAAAUUCAUUGAUUAUCGCACCUAAUGAUCACUAAACCCUGGGGGUUUCCUUGACUUUUUCCUAGAGUCUCACCCACGAAUAGU
..((((((........(((((((........)))))))........)))))).......((((((.....))))))............... ( -17.19)
>DroSec_CAF1 393 91 - 1
CUCCUCCAAAAUUCAUUGAUUAUCGUGCUUAGUGAUCACUAAACCCUGGGGGUUUCCUUGACUUUUUCCUAGAGUCUCAGCCACGAAUUGU
..((((((........(((((((........)))))))........)))))).......((((((.....))))))............... ( -17.49)
>DroSim_CAF1 418 91 - 1
CUCCUCCAAAAUUCAUUGAUUAUCGUACUUAGUGAUCACUAAACCCUGGGGGUUUCCUUGACUUUUUCCUAGAGUCUCACCCACGAAUUGU
..((((((........(((((((........)))))))........)))))).......((((((.....))))))............... ( -17.49)
>DroEre_CAF1 409 90 - 1
CUCCUCCAAA-GUCAUUGAUUAUCCCACUUAGUGAUCACAAAACCCUGGGGGUUUCCUUGACUCUUUCCUAGAGUCUCACCCACGAAUAGU
..((((((..-((...(((((((........)))))))....))..)))))).......((((((.....))))))............... ( -20.80)
>DroYak_CAF1 452 90 - 1
CUCCUCCAAA-CUCAUUGAUUAUCACACUUAGUGAUCACAAAACCCUGGGGGUUUCCUUGACUUUUUCUUAGAGUCUCACCCACAAAUAGU
..((((((..-....(((...(((((.....)))))..))).....)))))).......((((((.....))))))............... ( -17.20)
>DroAna_CAF1 336 84 - 1
CCGCCCCGUAGGCGGUUUAUUAUCUCAUUAAAUGAUCACCCAA-------GUGUUCAAUGAAUUUUGGCCAAUUUCCCACCCUCAAGUAAC
(((((.....))))).(((((...........(((.(((....-------))).))).(((....(((........)))...)))))))). ( -14.00)
>consensus
CUCCUCCAAAAUUCAUUGAUUAUCGCACUUAGUGAUCACUAAACCCUGGGGGUUUCCUUGACUUUUUCCUAGAGUCUCACCCACGAAUAGU
..((((((........(((((((........)))))))........)))))).......((((((.....))))))............... (-14.51 = -14.46 +  -0.05)

alignment

secondary structure

dotplot

Window 1

Location	3,270,269 – 3,270,361
Length	92
Sequences	6
Columns	92
Reading direction	reverse
Mean pairwise identity	80.57
Mean single sequence MFE	-21.68
Consensus MFE	-11.62
Energy contribution	-12.87
Covariance contribution	1.25
Combinations/Pair	1.14
Mean z-score	-1.95
Structure conservation index	0.54
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3270269 92 - 23771897
UUGGAGUUGCGUGUAAAAUUUACAACCAACUCCUCCAAAAUUCAUUGAUUAUCGCACCUAAUGAUCACUAAACCCUGGGGGUUUCCUUGACU
..(((((((..((((.....))))..)))))))........(((.(((((((........)))))))..((((((...))))))...))).. ( -21.80)
>DroSec_CAF1 421 91 - 1
UU-GAGUUGCGUGUAUAAUUUACAACCAACUCCUCCAAAAUUCAUUGAUUAUCGUGCUUAGUGAUCACUAAACCCUGGGGGUUUCCUUGACU
..-((((((..((((.....))))..))))))(((((........(((((((........)))))))........)))))............ ( -20.09)
>DroSim_CAF1 446 92 - 1
UUGGAGUUGCGUGUAUAAUUUACAACCAACUCCUCCAAAAUUCAUUGAUUAUCGUACUUAGUGAUCACUAAACCCUGGGGGUUUCCUUGACU
..(((((((..((((.....))))..)))))))........(((.(((((((........)))))))..((((((...))))))...))).. ( -22.90)
>DroEre_CAF1 437 91 - 1
UGGGUGUUGCGUGUAAAAUUCCCAAGCAACUCCUCCAAA-GUCAUUGAUUAUCCCACUUAGUGAUCACAAAACCCUGGGGGUUUCCUUGACU
.(((.(((((.((.........)).))))).)))....(-((((.(((((((........)))))))..((((((...))))))...))))) ( -22.90)
>DroYak_CAF1 480 91 - 1
UUUGUGUUGCGUGUAAAAUUUGCAACCAACUCCUCCAAA-CUCAUUGAUUAUCACACUUAGUGAUCACAAAACCCUGGGGGUUUCCUUGACU
.(((.((((((.........)))))))))..((((((..-....(((...(((((.....)))))..))).....))))))........... ( -19.60)
>DroAna_CAF1 364 85 - 1
GGGGAGUUGCGUGUAAAAUUCUCCAACAUCCGCCCCGUAGGCGGUUUAUUAUCUCAUUAAAUGAUCACCCAA-------GUGUUCAAUGAAU
((((((((........)))))))).....(((((.....))))).........((((....(((.(((....-------))).))))))).. ( -22.80)
>consensus
UUGGAGUUGCGUGUAAAAUUUACAACCAACUCCUCCAAAAUUCAUUGAUUAUCGCACUUAGUGAUCACUAAACCCUGGGGGUUUCCUUGACU
.....((((..((((.....))))..)))).((((((........(((((((........)))))))........))))))........... (-11.62 = -12.87 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:27 2006