Locus 6894

Sequence ID	X_DroMel_CAF1
Location	17,246,867 – 17,247,066
Length	199
Max. P	0.983944

overview

Window 5

Location	17,246,867 – 17,246,986
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.98
Mean single sequence MFE	-38.02
Consensus MFE	-32.28
Energy contribution	-32.24
Covariance contribution	-0.04
Combinations/Pair	1.08
Mean z-score	-1.48
Structure conservation index	0.85
SVM decision value	0.65
SVM RNA-class probability	0.811929
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17246867 119 + 22224390
-GGGUAGGAGAAUUGCCCCCUGCUAAGUGACAAUUAUUCGUGCUAGUUGUCGGUUUGGUUCUCCAAAGUAUUGGUUUCGUUACGCGAUUGGUUAGCGUUAAGUGGACGCCAAUCGCAUUU
-.....(((((((((..((((....)).((((((((.......))))))))))..)))))))))...(((.((....)).)))(((((((((..((.....))....))))))))).... ( -36.20)
>DroSec_CAF1 92545 119 + 1
-GGGUGGUAGGAUUGCGCCCUGCUAAGUGACAAUUAUUCGUGCUAGUUGUCGGUUUGGUUCUCCAAAGUAUUGGUUUCGUUACGCGAUUGGUUAGCGUUAAGUGGACGCCAAUCGCAUUU
-(((((.........))))).(((((..((((((((.......))))))))(.(((((....))))).).)))))........(((((((((..((.....))....))))))))).... ( -35.90)
>DroSim_CAF1 94978 119 + 1
-GGGUGGUAGGAUUGCCCCCUGCUAAGUGACAAUUAUUCGUGCUAGUUGUCGGUUUGGUUCUCCAAAGUAUUGGUUUCGUUACGCGAUUGGUUAGCGUUAAGUGGACGCCAAUCGCGUUU
-(((.((((....))))))).(((((..((((((((.......))))))))(.(((((....))))).).)))))......(((((((((((..((.....))....))))))))))).. ( -39.90)
>DroEre_CAF1 98865 119 + 1
GUGGAAGUGGGAUUGCC-CCUGCUAAGUGACAAUUAUUCGUGCUAGUUGUCGGUUUGGUUCUCCAAAGUAUUGGUUACGUUACGCGAUUGGCUGGCGUUAAGUGGACGCCAAUCGCAUUU
.((((((..((......-))..))((.(((((((((.......))))))))).))......))))..(((.((....)).)))((((((((((.((.....)).)..))))))))).... ( -37.40)
>DroYak_CAF1 102029 120 + 1
NNNGAAGGGGGAUUGCCCCCUGCUAAGUGACAAUUAUUCGUGCUAGUUGUCGGUUUGGUUCUCCAAAGUAUUGGUUACGUUACGCGAUUGGUUAGCGUUAAGUGGACGCCAAUCGCAUUU
.....((((((....))))))(((((..((((((((.......))))))))(.(((((....))))).).)))))........(((((((((..((.....))....))))))))).... ( -40.70)
>consensus
_GGGUAGUAGGAUUGCCCCCUGCUAAGUGACAAUUAUUCGUGCUAGUUGUCGGUUUGGUUCUCCAAAGUAUUGGUUUCGUUACGCGAUUGGUUAGCGUUAAGUGGACGCCAAUCGCAUUU
.....((((((.......))))))...(((((((((.......))))))))).(((((....)))))(((.((....)).)))(((((((((..((.....))....))))))))).... (-32.28 = -32.24 +  -0.04)

alignment

secondary structure

dotplot

Window 6

Location	17,246,867 – 17,246,986
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.98
Mean single sequence MFE	-28.99
Consensus MFE	-24.16
Energy contribution	-24.00
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.12
Structure conservation index	0.83
SVM decision value	1.90
SVM RNA-class probability	0.981881
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17246867 119 - 22224390
AAAUGCGAUUGGCGUCCACUUAACGCUAACCAAUCGCGUAACGAAACCAAUACUUUGGAGAACCAAACCGACAACUAGCACGAAUAAUUGUCACUUAGCAGGGGGCAAUUCUCCUACCC-
..(((((((((((((.......))))....))))))))).................((((((.....(((((((.((.......)).))))).((.....))))....)))))).....- ( -27.80)
>DroSec_CAF1 92545 119 - 1
AAAUGCGAUUGGCGUCCACUUAACGCUAACCAAUCGCGUAACGAAACCAAUACUUUGGAGAACCAAACCGACAACUAGCACGAAUAAUUGUCACUUAGCAGGGCGCAAUCCUACCACCC-
......(((((.(((((.....((((.........)))).......((((....))))...........(((((.((.......)).)))))........)))))))))).........- ( -25.10)
>DroSim_CAF1 94978 119 - 1
AAACGCGAUUGGCGUCCACUUAACGCUAACCAAUCGCGUAACGAAACCAAUACUUUGGAGAACCAAACCGACAACUAGCACGAAUAAUUGUCACUUAGCAGGGGGCAAUCCUACCACCC-
..(((((((((((((.......))))....))))))))).......((((....))))...........(((((.((.......)).)))))........(((((........)).)))- ( -29.00)
>DroEre_CAF1 98865 119 - 1
AAAUGCGAUUGGCGUCCACUUAACGCCAGCCAAUCGCGUAACGUAACCAAUACUUUGGAGAACCAAACCGACAACUAGCACGAAUAAUUGUCACUUAGCAGG-GGCAAUCCCACUUCCAC
..(((((((((((...............)))))))))))................(((((.........(((((.((.......)).)))))........((-(.....)))..))))). ( -30.46)
>DroYak_CAF1 102029 120 - 1
AAAUGCGAUUGGCGUCCACUUAACGCUAACCAAUCGCGUAACGUAACCAAUACUUUGGAGAACCAAACCGACAACUAGCACGAAUAAUUGUCACUUAGCAGGGGGCAAUCCCCCUUCNNN
..(((((((((((((.......))))....)))))))))...((..((((....))))...........(((((.((.......)).))))).....))((((((....))))))..... ( -32.60)
>consensus
AAAUGCGAUUGGCGUCCACUUAACGCUAACCAAUCGCGUAACGAAACCAAUACUUUGGAGAACCAAACCGACAACUAGCACGAAUAAUUGUCACUUAGCAGGGGGCAAUCCUACUACCC_
..(((((((((((((.......))))....))))))))).......((.....(((((....)))))..(((((.((.......)).)))))........)).................. (-24.16 = -24.00 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	17,246,906 – 17,247,026
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.08
Mean single sequence MFE	-29.07
Consensus MFE	-25.08
Energy contribution	-25.04
Covariance contribution	-0.04
Combinations/Pair	1.13
Mean z-score	-1.92
Structure conservation index	0.86
SVM decision value	1.96
SVM RNA-class probability	0.983944
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17246906 120 - 22224390
GUUAAUAUAAUUAGGCGGGAAUUACUUCGCUCUGAUCACCAAAUGCGAUUGGCGUCCACUUAACGCUAACCAAUCGCGUAACGAAACCAAUACUUUGGAGAACCAAACCGACAACUAGCA
((((......(((((((((......))))).))))((.....(((((((((((((.......))))....))))))))).......((((....)))).))..............)))). ( -27.10)
>DroSec_CAF1 92584 120 - 1
GUUAAUAUAAUUAGGCGGGAAUUACUCAGCUCUGAUCACCAAAUGCGAUUGGCGUCCACUUAACGCUAACCAAUCGCGUAACGAAACCAAUACUUUGGAGAACCAAACCGACAACUAGCA
((((......(((((((((.....))).)).))))((.....(((((((((((((.......))))....))))))))).......((((....)))).))..............)))). ( -25.30)
>DroSim_CAF1 95017 120 - 1
GUUAAUAUAAUUAGGCGGGAAUUACUCCGCUCUGAUCACCAAACGCGAUUGGCGUCCACUUAACGCUAACCAAUCGCGUAACGAAACCAAUACUUUGGAGAACCAAACCGACAACUAGCA
((((......(((((((((......))))).))))((.....(((((((((((((.......))))....))))))))).......((((....)))).))..............)))). ( -31.70)
>DroEre_CAF1 98904 118 - 1
GUUAGCAUAAUUAGGCGGAAAUUA--CUGCUCCGAUCACCAAAUGCGAUUGGCGUCCACUUAACGCCAGCCAAUCGCGUAACGUAACCAAUACUUUGGAGAACCAAACCGACAACUAGCA
(((((........(((((......--)))))....((.(((((((((((((((...............)))))))))))...(((.....))).)))).)).............))))). ( -31.16)
>DroYak_CAF1 102069 120 - 1
GUCAACAUAAUUAGGCGGAAAUUACGCUGCUCCGAUCAGCAAAUGCGAUUGGCGUCCACUUAACGCUAACCAAUCGCGUAACGUAACCAAUACUUUGGAGAACCAAACCGACAACUAGCA
(((..........((((.......)))).((((((.......(((((((((((((.......))))....)))))))))...(((.....))).)))))).........)))........ ( -30.10)
>consensus
GUUAAUAUAAUUAGGCGGGAAUUACUCCGCUCUGAUCACCAAAUGCGAUUGGCGUCCACUUAACGCUAACCAAUCGCGUAACGAAACCAAUACUUUGGAGAACCAAACCGACAACUAGCA
(((.......((((((((........)))).))))((.....(((((((((((((.......))))....))))))))).......((((....)))).))........)))........ (-25.08 = -25.04 +  -0.04)

alignment

secondary structure

dotplot

Window 8

Location	17,246,946 – 17,247,066
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.42
Mean single sequence MFE	-32.96
Consensus MFE	-22.90
Energy contribution	-23.06
Covariance contribution	0.16
Combinations/Pair	1.27
Mean z-score	-1.97
Structure conservation index	0.69
SVM decision value	0.33
SVM RNA-class probability	0.690784
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17246946 120 + 22224390
UACGCGAUUGGUUAGCGUUAAGUGGACGCCAAUCGCAUUUGGUGAUCAGAGCGAAGUAAUUCCCGCCUAAUUAUAUUAACUUAAUGGUUUUAAAAGCAACUCAUGUCGAUUAUUAAAAAU
...(((((((((..((.....))....))))))))).((((((((((((.(((((....)))..))))...............((((((........))).)))...))))))))))... ( -28.20)
>DroSec_CAF1 92624 120 + 1
UACGCGAUUGGUUAGCGUUAAGUGGACGCCAAUCGCAUUUGGUGAUCAGAGCUGAGUAAUUCCCGCCUAAUUAUAUUAACUUAAUGGCUUUAAAAGGAACUCAAGCCGACUAUUAAGAAU
...(((((((((..((.....))....))))))))).(((((((.((.(.(((((((...(((.(((..((((........))))))).......))))))).)))))).)))))))... ( -29.60)
>DroSim_CAF1 95057 120 + 1
UACGCGAUUGGUUAGCGUUAAGUGGACGCCAAUCGCGUUUGGUGAUCAGAGCGGAGUAAUUCCCGCCUAAUUAUAUUAACUUAAUGGUUUUAAAAGGAACUCAAGCCGACUAUUAAGAAU
.(((((((((((..((.....))....)))))))))))...(((((.((.((((........)))))).))))).....((((((((((......((........))))))))))))... ( -37.20)
>DroEre_CAF1 98944 116 + 1
UACGCGAUUGGCUGGCGUUAAGUGGACGCCAAUCGCAUUUGGUGAUCGGAGCAG--UAAUUUCCGCCUAAUUAUGCUAACUUAAUGCCCUAG--AACCACUCAGGCCGAUUAUCAAAAAU
...((((((((((.((.....)).)..))))))))).((((((((((((((((.--(((((.......)))))))))..........(((.(--(.....)))))))))))))))))... ( -39.10)
>DroYak_CAF1 102109 120 + 1
UACGCGAUUGGUUAGCGUUAAGUGGACGCCAAUCGCAUUUGCUGAUCGGAGCAGCGUAAUUUCCGCCUAAUUAUGUUGACCUAAUGAUUUUGAAAACUACUCAUGCUGAUUUUUAAAAAG
...(((((((((..((.....))....))))))))).((((..((((((..((((((((((.......)))))))))).....((((.............)))).))))))..))))... ( -30.72)
>consensus
UACGCGAUUGGUUAGCGUUAAGUGGACGCCAAUCGCAUUUGGUGAUCAGAGCAGAGUAAUUCCCGCCUAAUUAUAUUAACUUAAUGGUUUUAAAAGCAACUCAAGCCGAUUAUUAAAAAU
...(((((((((..((.....))....))))))))).((((((((((((.((............)))).................(((((............)))))))))))))))... (-22.90 = -23.06 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:23 2006