Locus 6312

Sequence ID	2L_DroMel_CAF1
Location	17,588,426 – 17,588,562
Length	136
Max. P	0.920247

overview

Window 7

Location	17,588,426 – 17,588,524
Length	98
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	73.20
Mean single sequence MFE	-20.72
Consensus MFE	-10.73
Energy contribution	-12.26
Covariance contribution	1.53
Combinations/Pair	1.20
Mean z-score	-1.96
Structure conservation index	0.52
SVM decision value	1.13
SVM RNA-class probability	0.920247
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17588426 98 - 22407834
AUGCUCGUCUUUACGAGCAUAUUCGG-----AAAUUGACUCA-UAUGAGUACGAGUGACCACAAAACAUUAUUGCAAAAUCUCGCAAUCUCAGUGCAAUGCCUA
((((((((....))))))))....((-----...(((((((.-...)))).)))....))......(((((((((........)))))...))))......... ( -21.70)
>DroSec_CAF1 105182 98 - 1
AUGCUCGUCUUUAUGAGCAUAUUCGG-----AAAUUGACUCA-UAUGAGUGCAAGUGACCACAAAACAUUAUUGCACAAUCUCGCAAUCUCAGUGCAAUGCCUA
((((((((....))))))))....((-----...(((((((.-...)))).)))....)).........((((((((...............)))))))).... ( -23.56)
>DroSim_CAF1 104268 98 - 1
AUGCUCGUCUUUACGAGCAUAUUCGG-----AAAUUGACUCA-UAUGAGUGCGAGUGACCACAAAACAUUAUUGCACAAUCUCGCAAUCUCAGUGCAAUGCCUA
((((((((....))))))))....((-----...(((((((.-...)))).)))....)).........((((((((...............)))))))).... ( -25.06)
>DroEre_CAF1 103392 85 - 1
AUGCUCGUCUCUACGAGCAUAUUUCG-----AAAUUGACUCA-----CAUGCGUUUA---------CAUAGUUGCACAAUCUCCCAAUCCCAGUGCAACGCCUA
((((((((....))))))))......-----...........-----..........---------....(((((((...............)))))))..... ( -19.66)
>DroYak_CAF1 106078 98 - 1
AUGCUCGUCUUUACGAGCAUAUUCGG-----AAAUUGACUCA-UGUACAUGCGAGUACCCACAAAACAUUAUUGCACAAUCUCUUAAUCUCAGUGCAAUGCCUA
((((((((....))))))))....((-----...........-.((((......))))...........((((((((...............)))))))))).. ( -21.96)
>DroAna_CAF1 109670 86 - 1
GUGCUCAUCU------GCCAAUUCAGCUAAUAAAUUGACUCAAUUUUUUUACUCGUGGCU----CAUUUUAUU--------ACCUAAUCUCGGUGCGAAUCACG
(((.((....------((((....((..((.((((((...)))))).))..))..)))).----........(--------(((.......)))).))..))). ( -12.40)
>consensus
AUGCUCGUCUUUACGAGCAUAUUCGG_____AAAUUGACUCA_UAUGAGUGCGAGUGACCACAAAACAUUAUUGCACAAUCUCGCAAUCUCAGUGCAAUGCCUA
((((((((....))))))))..................................................(((((((...............)))))))..... (-10.73 = -12.26 +   1.53)

alignment

secondary structure

dotplot

Window 8

Location	17,588,463 – 17,588,562
Length	99
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	70.15
Mean single sequence MFE	-23.49
Consensus MFE	-9.79
Energy contribution	-11.65
Covariance contribution	1.86
Combinations/Pair	1.06
Mean z-score	-1.74
Structure conservation index	0.42
SVM decision value	0.18
SVM RNA-class probability	0.620202
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17588463 99 + 22407834
GUUUUGUGGUCACUCGUACUCAUA-UGAGUCAAUUU-----CCGAAUAUGCUCGUAAAGACGAGCAUAAAUUAUA--UAUUUCUCUGUUAAUCGGAUUGCUCAGUGA
...................((((.-((((.(((..(-----((((.(((((((((....)))))))))(((....--.)))..........)))))))))))))))) ( -23.90)
>DroSec_CAF1 105219 99 + 1
GUUUUGUGGUCACUUGCACUCAUA-UGAGUCAAUUU-----CCGAAUAUGCUCAUAAAGACGAGCAUAAAUUAUA--UAUUUCUCUGCCAAUCGGGUUGCUCAACGA
(((..(..(....(((.((((...-.)))))))..(-----((((.(((((((........)))))))(((....--.)))..........))))))..)..))).. ( -19.80)
>DroSim_CAF1 104305 99 + 1
GUUUUGUGGUCACUCGCACUCAUA-UGAGUCAAUUU-----CCGAAUAUGCUCGUAAAGACGAGCAUAAAUUAUA--UAUUUCUCUGUGAAUCGGGUUGCUCAAUGA
....(((((....))))).((((.-((((.((((..-----((((.(((((((((....)))))))))..(((((--........))))).)))))))))))))))) ( -28.70)
>DroEre_CAF1 103429 88 + 1
G---------UAAACGCAUG-----UGAGUCAAUUU-----CGAAAUAUGCUCGUAGAGACGAGCAUAAUUUAUAUAUAUUUCUCUUGGAAGCGGGUUGCUCACUGA
.---------......((.(-----((((.(((((.-----((...(((((((((....)))))))))...........((((....)))).)))))))))))))). ( -25.10)
>DroYak_CAF1 106115 99 + 1
GUUUUGUGGGUACUCGCAUGUACA-UGAGUCAAUUU-----CCGAAUAUGCUCGUAAAGACGAGCAUAAUUUAUA--UAUUUCUCGUGGAAUCGGGUUGCUUAAUGA
......((((((((((.((...((-((((.......-----.....(((((((((....))))))))).......--.....))))))..)))))).)))))).... ( -28.85)
>DroAna_CAF1 109699 85 + 1
AUG----AGCCACGAGUAAAAAAAUUGAGUCAAUUUAUUAGCUGAAUUGGC------AGAUGAGCACU------------UUUUCAAACUAUGCGUCUUCUCAGUGA
.((----((..(((.(((..........(((((((((.....)))))))))------...((((....------------..))))...))).)))...)))).... ( -14.60)
>consensus
GUUUUGUGGUCACUCGCACUCAUA_UGAGUCAAUUU_____CCGAAUAUGCUCGUAAAGACGAGCAUAAAUUAUA__UAUUUCUCUGGGAAUCGGGUUGCUCAAUGA
.........................(((((................(((((((((....)))))))))..............(((........)))..))))).... ( -9.79 = -11.65 +   1.86)

alignment

secondary structure

dotplot

Window 9

Location	17,588,463 – 17,588,562
Length	99
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	70.15
Mean single sequence MFE	-20.70
Consensus MFE	-9.09
Energy contribution	-10.23
Covariance contribution	1.14
Combinations/Pair	1.19
Mean z-score	-1.84
Structure conservation index	0.44
SVM decision value	0.64
SVM RNA-class probability	0.809412
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17588463 99 - 22407834
UCACUGAGCAAUCCGAUUAACAGAGAAAUA--UAUAAUUUAUGCUCGUCUUUACGAGCAUAUUCGG-----AAAUUGACUCA-UAUGAGUACGAGUGACCACAAAAC
(((((......(((((.......(....).--.......(((((((((....))))))))).))))-----).....((((.-...))))...)))))......... ( -24.90)
>DroSec_CAF1 105219 99 - 1
UCGUUGAGCAACCCGAUUGGCAGAGAAAUA--UAUAAUUUAUGCUCGUCUUUAUGAGCAUAUUCGG-----AAAUUGACUCA-UAUGAGUGCAAGUGACCACAAAAC
(((((((((((.((((.......(....).--.......(((((((((....))))))))).))))-----...))).))))-.))))(((........)))..... ( -21.50)
>DroSim_CAF1 104305 99 - 1
UCAUUGAGCAACCCGAUUCACAGAGAAAUA--UAUAAUUUAUGCUCGUCUUUACGAGCAUAUUCGG-----AAAUUGACUCA-UAUGAGUGCGAGUGACCACAAAAC
(((((..((...(((((((.....)))...--.......(((((((((....))))))))).))))-----......((((.-...)))))).)))))......... ( -25.60)
>DroEre_CAF1 103429 88 - 1
UCAGUGAGCAACCCGCUUCCAAGAGAAAUAUAUAUAAAUUAUGCUCGUCUCUACGAGCAUAUUUCG-----AAAUUGACUCA-----CAUGCGUUUA---------C
...((((((((....(((....)))..............(((((((((....))))))))).....-----...))).))))-----).........---------. ( -20.00)
>DroYak_CAF1 106115 99 - 1
UCAUUAAGCAACCCGAUUCCACGAGAAAUA--UAUAAAUUAUGCUCGUCUUUACGAGCAUAUUCGG-----AAAUUGACUCA-UGUACAUGCGAGUACCCACAAAAC
.......(((..(((((((.....)))...--.......(((((((((....))))))))).))))-----....((((...-.)).)))))............... ( -19.20)
>DroAna_CAF1 109699 85 - 1
UCACUGAGAAGACGCAUAGUUUGAAAA------------AGUGCUCAUCU------GCCAAUUCAGCUAAUAAAUUGACUCAAUUUUUUUACUCGUGGCU----CAU
......(((.((.((((...((....)------------))))))).)))------((((....((..((.((((((...)))))).))..))..)))).----... ( -13.00)
>consensus
UCAUUGAGCAACCCGAUUCACAGAGAAAUA__UAUAAUUUAUGCUCGUCUUUACGAGCAUAUUCGG_____AAAUUGACUCA_UAUGAGUGCGAGUGACCACAAAAC
......................(((..............(((((((((....))))))))).((((........))))))).......................... ( -9.09 = -10.23 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:01 2006