Locus 2308

Sequence ID	2R_DroMel_CAF1
Location	8,494,200 – 8,494,435
Length	235
Max. P	0.991310

overview

Window 9

Location	8,494,200 – 8,494,315
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.96
Mean single sequence MFE	-27.78
Consensus MFE	-19.56
Energy contribution	-20.12
Covariance contribution	0.56
Combinations/Pair	1.12
Mean z-score	-2.43
Structure conservation index	0.70
SVM decision value	0.78
SVM RNA-class probability	0.849423
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8494200 115 - 20766785
UCUUCGCGCACCAACGAGGCUAUACCGAU----AUAGCUUCGGCUUAUUGCUUUCUGCGGCUCAGCGUCUGAUUUAUUUAUAAUCUUCAGCACGCUCUCUUCUCGAGUCGAUUUACAUU-
...((..(((....((((((((((....)----)))))))))((.....))....)))((((((((((((((..............)))).)))))........)))))))........- ( -31.94)
>DroSec_CAF1 6551 115 - 1
UCUUCGCGCACCAACGAGGCUAUACCGAU----AUAGCUUCAGCUUAUUGCUUUCUGCGGCUCAGCGGCUGAUUUAUUUAUAAUCUUCAGCACGCUCUCUUCUCAAGUCGAUUUUCAUU-
...(((((((.....(((((((((....)----))))))))(((.....)))...))))....(((((((((..............))))).))))............)))........- ( -30.04)
>DroSim_CAF1 6469 115 - 1
UCUUCGCGCACCAACGAGGCUUUACCAAU----AUAGCUUCAGCUUAUUGCUUUCUGCGGCUCAGCGGCUGAUUUAUUUAUAAUCUUCAGCACGCUCUCUUCUCAAGUCGAUUUUCAUU-
...(((((((.....((((((........----..))))))(((.....)))...))))....(((((((((..............))))).))))............)))........- ( -26.14)
>DroEre_CAF1 4014 112 - 1
UUGC--CCCACCAACGAAGCUACA--GAU----AUAGCUUCAGCUUAUUGCUUUCUGCGGCUCAGCCGCUGAUUUAUUUAUAAUCUUCAGCACGCUCUCGUCUCAAGUCGAUUUUGAAUU
..((--(.((.....(((((((..--...----.)))))))(((.....)))...)).)))(((((.(((((..............)))))..))..(((.(....).)))...)))... ( -25.14)
>DroYak_CAF1 6760 118 - 1
UCUC--CCCAUCAACGAAGCUACACAGAUAUAUGUAGCUUCAGCUUAUUGCUUUCUGCGGCUCAACCGCUGAUUUAUUAAUAAUCUUCAGCACGCUCUCGUCUCAAGUCGAUUUUCGUUU
....--.........(((((((((........)))))))))(((.....)))....((((.....))(((((..............)))))..))..(((.(....).)))......... ( -25.64)
>consensus
UCUUCGCGCACCAACGAGGCUAUACCGAU____AUAGCUUCAGCUUAUUGCUUUCUGCGGCUCAGCGGCUGAUUUAUUUAUAAUCUUCAGCACGCUCUCUUCUCAAGUCGAUUUUCAUU_
...............((((((((..........))))))))(((.....))).....(((((.(((((((((..............))))).)))).........))))).......... (-19.56 = -20.12 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	8,494,239 – 8,494,355
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.69
Mean single sequence MFE	-39.22
Consensus MFE	-30.74
Energy contribution	-30.70
Covariance contribution	-0.04
Combinations/Pair	1.09
Mean z-score	-2.83
Structure conservation index	0.78
SVM decision value	2.26
SVM RNA-class probability	0.991310
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8494239 116 - 20766785
UUCUAUCGUAAACAGCGAGGGGCGAGUGGAGCUUUAAGCUUCUUCGCGCACCAACGAGGCUAUACCGAU----AUAGCUUCGGCUUAUUGCUUUCUGCGGCUCAGCGUCUGAUUUAUUUA
.......((((((((((..(((((((.(((((.....)))))))).((((....((((((((((....)----)))))))))((.....))....))))))))..)).))).)))))... ( -40.40)
>DroSec_CAF1 6590 116 - 1
UUCUUUCGUAAACAGCGAGGGGCGAGUGGAGCUUUAAGCUUCUUCGCGCACCAACGAGGCUAUACCGAU----AUAGCUUCAGCUUAUUGCUUUCUGCGGCUCAGCGGCUGAUUUAUUUA
.......((((((((((..(.(((((.(((((.....)))))))))).)..)...(((((((((....)----)))))))).(((..((((.....))))...))).)))).)))))... ( -39.50)
>DroSim_CAF1 6508 116 - 1
UUCUUUCGUAAACAGCGAGGGGCGAGUGGAGCUUUAAGCUUCUUCGCGCACCAACGAGGCUUUACCAAU----AUAGCUUCAGCUUAUUGCUUUCUGCGGCUCAGCGGCUGAUUUAUUUA
.......((((((((((..(.(((((.(((((.....)))))))))).)..)...((((((........----..)))))).(((..((((.....))))...))).)))).)))))... ( -35.60)
>DroEre_CAF1 4054 112 - 1
UUCUUUCGUAAACAGCGUGGGGCGAGUGGAGCUUUAAGCUUUGC--CCCACCAACGAAGCUACA--GAU----AUAGCUUCAGCUUAUUGCUUUCUGCGGCUCAGCCGCUGAUUUAUUUA
.......((((..((((((((((((....(((.....)))))))--)))))....(((((((..--...----.))))))).)))..))))..((.(((((...))))).))........ ( -41.70)
>DroYak_CAF1 6800 118 - 1
UUCUUUCGUAAACAGCGAGGGGCGAUUGGAGCUUUAAGCUUCUC--CCCAUCAACGAAGCUACACAGAUAUAUGUAGCUUCAGCUUAUUGCUUUCUGCGGCUCAACCGCUGAUUUAUUAA
.......((((((((((.(((.((...(((((..((((((....--.........(((((((((........)))))))))))))))..)))))...)).)))...))))).)))))... ( -38.91)
>consensus
UUCUUUCGUAAACAGCGAGGGGCGAGUGGAGCUUUAAGCUUCUUCGCGCACCAACGAGGCUAUACCGAU____AUAGCUUCAGCUUAUUGCUUUCUGCGGCUCAGCGGCUGAUUUAUUUA
.......(((((((((..(((.((...(((((..((((((...............((((((((..........))))))))))))))..)))))...)).)))....)))).)))))... (-30.74 = -30.70 +  -0.04)

alignment

secondary structure

dotplot

Window 1

Location	8,494,315 – 8,494,435
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.16
Mean single sequence MFE	-33.20
Consensus MFE	-29.88
Energy contribution	-30.08
Covariance contribution	0.20
Combinations/Pair	1.05
Mean z-score	-1.74
Structure conservation index	0.90
SVM decision value	1.79
SVM RNA-class probability	0.977400
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8494315 120 - 20766785
GUGAGGAAAAAUACGAUCCCACCGAGUUCAUUAACUCUACCAGUUUUCCCAGAAAGUGUAUAUUUCCCUUGCCUCCAUUAUUCUAUCGUAAACAGCGAGGGGCGAGUGGAGCUUUAAGCU
(..((((((.(((((........(((((....)))))......(((((...)))))))))).))).)))..)(((((((..(((.((((.....)))).)))..)))))))......... ( -27.90)
>DroSec_CAF1 6666 120 - 1
GCGAGGAAAAAUACGAUCCCACCGAGUUCAUUAACUCGACCAGUUUUCCCAGAAAAUGUAUAUUUCCCUUGCCUCCAUUAUUCUUUCGUAAACAGCGAGGGGCGAGUGGAGCUUUAAGCU
(((((((((.((((........((((((....))))))....((((((...)))))))))).))).))))))(((((((..((((((((.....))))))))..)))))))......... ( -36.90)
>DroSim_CAF1 6584 120 - 1
GCGAGGAAAAAUACGAUCCCACCGAGUUCAUUAACUCGACCAGUUUUCCCAGAAAAUGUAUAUUUCCCUUGCCUCCAUUAUUCUUUCGUAAACAGCGAGGGGCGAGUGGAGCUUUAAGCU
(((((((((.((((........((((((....))))))....((((((...)))))))))).))).))))))(((((((..((((((((.....))))))))..)))))))......... ( -36.90)
>DroEre_CAF1 4126 119 - 1
GUGAGGAAAAAUACGAUCCCACCGAGUUCAUUAACUCUGCGAGUUUUCCCAGAAAAUGUAUAUUUCCCUUGC-UCCAUUAUUCUUUCGUAAACAGCGUGGGGCGAGUGGAGCUUUAAGCU
....(((((.((((.........(((((....))))).....((((((...)))))))))).)))))...((-((((((..(((..(((.....)))..)))..))))))))........ ( -30.70)
>DroYak_CAF1 6878 119 - 1
GCGAGGAAAAAUACGAUCCCACCGAGUUCAUUAACUCUGCGAGUUUUCCCAGAAAAUGUAUAUUUCCCUUGC-UCCAUUAUUCUUUCGUAAACAGCGAGGGGCGAUUGGAGCUUUAAGCU
((..(((((.((((.........(((((....))))).....((((((...)))))))))).)))))...((-((((....((((((((.....))))))))....)))))).....)). ( -33.60)
>consensus
GCGAGGAAAAAUACGAUCCCACCGAGUUCAUUAACUCUACCAGUUUUCCCAGAAAAUGUAUAUUUCCCUUGCCUCCAUUAUUCUUUCGUAAACAGCGAGGGGCGAGUGGAGCUUUAAGCU
(((((((((.((((.........(((((....))))).....((((((...)))))))))).))).)))))).((((((..((((((((.....))))))))..))))))((.....)). (-29.88 = -30.08 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:26 2006