Locus 8274

Sequence ID	3L_DroMel_CAF1
Location	21,727,092 – 21,727,271
Length	179
Max. P	0.999694

overview

Window 1

Location	21,727,092 – 21,727,191
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.21
Mean single sequence MFE	-23.67
Consensus MFE	-12.93
Energy contribution	-13.40
Covariance contribution	0.47
Combinations/Pair	1.19
Mean z-score	-1.76
Structure conservation index	0.55
SVM decision value	0.57
SVM RNA-class probability	0.783873
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21727092 99 + 23771897
UUUGGUUUUGCGUUUUUUCCUACUCCUCGC---------------UGGAGUGGCUA------CUGUUGACUUGUCAAGGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCC
..(((((((((........(((((((....---------------.)))))))...------...((((....)))).((((...(((......)))...)))).)))..)))))).... ( -24.70)
>DroPse_CAF1 35899 116 + 1
GCCAGCU----CUCUUCAUCUAUUUCUCAACUUUUUUUAACCUUUUCCAGUUGCCACUGCAGCUGAUCACUUGUCAUAGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCC
(((....----....................................(((((((....))))))).............((((...(((......)))...)))))))............. ( -22.60)
>DroSec_CAF1 8708 99 + 1
UUUGGUUUUGCGUUUUUUCCAACUUCUCAC---------------UGGAGUGGCUA------CUGUUGACUUGUCAAGGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCC
..((((((((((((......))).......---------------((((((((..(------((((.(((((......))))).)))))))))))))........)))..)))))).... ( -22.70)
>DroSim_CAF1 13748 99 + 1
UUUGGUUUUGCGUUUUUUCCAACUUCUCAC---------------UGGAGUGGCUA------CUGUUGACUUGUCAAGGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCC
..((((((((((((......))).......---------------((((((((..(------((((.(((((......))))).)))))))))))))........)))..)))))).... ( -22.70)
>DroPer_CAF1 34471 116 + 1
GCCAGCU----CUCUUCAUCUAUUUCUCAACUUUUUUUAACCUUUUCCAGUUGCCACUGCAGCUGAUCACUUGUCAUAGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCC
(((....----....................................(((((((....))))))).............((((...(((......)))...)))))))............. ( -22.60)
>DroYak_CAF1 59476 94 + 1
UUUGGCU----GUCUUUUGCUACUACUCGG---------------UGGAGUGGCUA------CUGU-GAGUUGUCAAGGAGUUUAUGGUUCAUUCCACCUACUCGGCAAUAAAUCAUGCC
...((((----(....(((((.......((---------------((((((((..(------((((-((..(.......)..))))))))))))))))).....))))).....)).))) ( -26.70)
>consensus
UUUGGCU____GUCUUUUCCUACUUCUCAC_______________UGGAGUGGCUA______CUGUUGACUUGUCAAGGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCC
.............................................(((((((((((......((.((((....))))))......))).)))))))).......((((........)))) (-12.93 = -13.40 +   0.47)

alignment

secondary structure

dotplot

Window 2

Location	21,727,092 – 21,727,191
Length	99
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.21
Mean single sequence MFE	-23.18
Consensus MFE	-14.73
Energy contribution	-14.73
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.15
Structure conservation index	0.64
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21727092 99 - 23771897
GGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAACUCCUUGACAAGUCAACAG------UAGCCACUCCA---------------GCGAGGAGUAGGAAAAAACGCAAAACCAAA
((((........))))((((..((((......))))..)))).((((....))))...------...(((((((.---------------....))))).)).................. ( -24.80)
>DroPse_CAF1 35899 116 - 1
GGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAACUCUAUGACAAGUGAUCAGCUGCAGUGGCAACUGGAAAAGGUUAAAAAAAGUUGAGAAAUAGAUGAAGAG----AGCUGGC
((((........))))((((..((((......))))..))))............((((((.((((....))))................(((.(....).)))......----)))))). ( -25.20)
>DroSec_CAF1 8708 99 - 1
GGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAACUCCUUGACAAGUCAACAG------UAGCCACUCCA---------------GUGAGAAGUUGGAAAAAACGCAAAACCAAA
((((........))))((((..((((......))))..)))).((((....))))...------..(((((....---------------)))....(((......)))))......... ( -20.60)
>DroSim_CAF1 13748 99 - 1
GGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAACUCCUUGACAAGUCAACAG------UAGCCACUCCA---------------GUGAGAAGUUGGAAAAAACGCAAAACCAAA
((((........))))((((..((((......))))..)))).((((....))))...------..(((((....---------------)))....(((......)))))......... ( -20.60)
>DroPer_CAF1 34471 116 - 1
GGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAACUCUAUGACAAGUGAUCAGCUGCAGUGGCAACUGGAAAAGGUUAAAAAAAGUUGAGAAAUAGAUGAAGAG----AGCUGGC
((((........))))((((..((((......))))..))))............((((((.((((....))))................(((.(....).)))......----)))))). ( -25.20)
>DroYak_CAF1 59476 94 - 1
GGCAUGAUUUAUUGCCGAGUAGGUGGAAUGAACCAUAAACUCCUUGACAACUC-ACAG------UAGCCACUCCA---------------CCGAGUAGUAGCAAAAGAC----AGCCAAA
(((.((.(((.((((.((((..((((......))))..))))...........-....------..((.((((..---------------..)))).)).)))).))))----))))... ( -22.70)
>consensus
GGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAACUCCUUGACAAGUCAACAG______UAGCCACUCCA_______________GUGAGAAGUAGGAAAAAAC____AACCAAA
((((........))))((((..((((......))))..)))).............................................................................. (-14.73 = -14.73 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	21,727,122 – 21,727,231
Length	109
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	89.45
Mean single sequence MFE	-27.98
Consensus MFE	-22.23
Energy contribution	-22.90
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.69
Structure conservation index	0.79
SVM decision value	0.54
SVM RNA-class probability	0.774024
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21727122 109 + 23771897
-----UGGAGUGGCUA------CUGUUGACUUGUCAAGGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCUGACAACC
-----..(((((((.(------(..((((....)))).((((...(((......)))...))))((((........)))).........)).)))))))..................... ( -28.50)
>DroPse_CAF1 35935 120 + 1
CCUUUUCCAGUUGCCACUGCAGCUGAUCACUUGUCAUAGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCCAACAACC
...(((((((((((....))))))).......(.((((((((...(((......)))...))))((((........))))......)))).).............))))........... ( -25.50)
>DroSec_CAF1 8738 109 + 1
-----UGGAGUGGCUA------CUGUUGACUUGUCAAGGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCUGACAACC
-----..(((((((.(------(..((((....)))).((((...(((......)))...))))((((........)))).........)).)))))))..................... ( -28.50)
>DroSim_CAF1 13778 109 + 1
-----UGGAGUGGCUA------CUGUUGACUUGUCAAGGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCUGACAACC
-----..(((((((.(------(..((((....)))).((((...(((......)))...))))((((........)))).........)).)))))))..................... ( -28.50)
>DroPer_CAF1 34507 120 + 1
CCUUUUCCAGUUGCCACUGCAGCUGAUCACUUGUCAUAGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCCAACAACC
...(((((((((((....))))))).......(.((((((((...(((......)))...))))((((........))))......)))).).............))))........... ( -25.50)
>DroYak_CAF1 59502 108 + 1
-----UGGAGUGGCUA------CUGU-GAGUUGUCAAGGAGUUUAUGGUUCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCUGACAACC
-----..(((((((.(------(.((-((((((.....((((...(((......)))...))))((((........)))).)))))))))).)))))))..................... ( -31.40)
>consensus
_____UGGAGUGGCUA______CUGUUGACUUGUCAAGGAGUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCUGACAACC
.......(((((((........................((((...(((......)))...))))((((........))))............)))))))..................... (-22.23 = -22.90 +   0.67)

alignment

secondary structure

dotplot

Window 4

Location	21,727,151 – 21,727,271
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	96.78
Mean single sequence MFE	-23.97
Consensus MFE	-23.86
Energy contribution	-23.45
Covariance contribution	-0.41
Combinations/Pair	1.13
Mean z-score	-1.18
Structure conservation index	1.00
SVM decision value	1.92
SVM RNA-class probability	0.982755
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21727151 120 + 23771897
GUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCUGACAACCGAAUAUGGCGGCACGGUGCCAUAAUUUCAUAGCCAAGUUA
..(((((((((.............((((........))))........((((((((.((.....................))...)))))))).)).)))))))................ ( -25.00)
>DroPse_CAF1 35975 119 + 1
GUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCCAACAACCGAAUAUGGCGAUACGGUGCCAUAAUUUCAUAGCCA-GUAA
..(((((((((.............((((........))))........((((((((.((.....................))...)))))))).)).)))))))...........-.... ( -23.70)
>DroSec_CAF1 8767 120 + 1
GUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCUGACAACCGAAUAUGGCGGCACGGUGCCAUAAUUUCAUAGCCAAGUUA
..(((((((((.............((((........))))........((((((((.((.....................))...)))))))).)).)))))))................ ( -25.00)
>DroSim_CAF1 13807 120 + 1
GUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCUGACAACCGAAUAUGGCGGCACGGUGCCAUAAUUUCAUAGCCAAGUUA
..(((((((((.............((((........))))........((((((((.((.....................))...)))))))).)).)))))))................ ( -25.00)
>DroPer_CAF1 34547 119 + 1
GUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCCAACAACCGAAUAUGGCGAUACGGUGCCAUAAUUUCAUAGCCA-GUAA
..(((((((((.............((((........))))........((((((((.((.....................))...)))))))).)).)))))))...........-.... ( -23.70)
>DroYak_CAF1 59530 120 + 1
GUUUAUGGUUCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCUGACAACCGAAUAUGGCAGCACGGUGCCAUAAUUUCAUAGCCAAGUUA
.....(((((..............((((........))))........(((((....((......)).....)))))...((((((((((......)))))))..)))..)))))..... ( -21.40)
>consensus
GUUUAUGGUCCAUUCCACCUACUCGGCAAUAAAUCAUGCCUUAAUUUAUGUCGCCACUCAAUAACGAAACCCUGACAACCGAAUAUGGCGGCACGGUGCCAUAAUUUCAUAGCCAAGUUA
..(((((((((.............((((........))))........((((((((.((.....................))...)))))))).)).)))))))................ (-23.86 = -23.45 +  -0.41)

alignment

secondary structure

dotplot

Window 5

Location	21,727,151 – 21,727,271
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.78
Mean single sequence MFE	-36.62
Consensus MFE	-35.40
Energy contribution	-34.77
Covariance contribution	-0.64
Combinations/Pair	1.11
Mean z-score	-2.14
Structure conservation index	0.97
SVM decision value	3.90
SVM RNA-class probability	0.999694
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21727151 120 - 23771897
UAACUUGGCUAUGAAAUUAUGGCACCGUGCCGCCAUAUUCGGUUGUCAGGGUUUCGUUAUUGAGUGGCGACAUAAAUUAAGGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAAC
................((((((..((((.(((((.(((((.(((((((....((((....))))))))))).........((((........)))))))))))))).)))).)))))).. ( -38.30)
>DroPse_CAF1 35975 119 - 1
UUAC-UGGCUAUGAAAUUAUGGCACCGUAUCGCCAUAUUCGGUUGUUGGGGUUUCGUUAUUGAGUGGCGACAUAAAUUAAGGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAAC
....-...........((((((..((((.(((((.((((((((..........(((((((...))))))).((((((((.....)))))))).))))))))))))).)))).)))))).. ( -34.10)
>DroSec_CAF1 8767 120 - 1
UAACUUGGCUAUGAAAUUAUGGCACCGUGCCGCCAUAUUCGGUUGUCAGGGUUUCGUUAUUGAGUGGCGACAUAAAUUAAGGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAAC
................((((((..((((.(((((.(((((.(((((((....((((....))))))))))).........((((........)))))))))))))).)))).)))))).. ( -38.30)
>DroSim_CAF1 13807 120 - 1
UAACUUGGCUAUGAAAUUAUGGCACCGUGCCGCCAUAUUCGGUUGUCAGGGUUUCGUUAUUGAGUGGCGACAUAAAUUAAGGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAAC
................((((((..((((.(((((.(((((.(((((((....((((....))))))))))).........((((........)))))))))))))).)))).)))))).. ( -38.30)
>DroPer_CAF1 34547 119 - 1
UUAC-UGGCUAUGAAAUUAUGGCACCGUAUCGCCAUAUUCGGUUGUUGGGGUUUCGUUAUUGAGUGGCGACAUAAAUUAAGGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAAC
....-...........((((((..((((.(((((.((((((((..........(((((((...))))))).((((((((.....)))))))).))))))))))))).)))).)))))).. ( -34.10)
>DroYak_CAF1 59530 120 - 1
UAACUUGGCUAUGAAAUUAUGGCACCGUGCUGCCAUAUUCGGUUGUCAGGGUUUCGUUAUUGAGUGGCGACAUAAAUUAAGGCAUGAUUUAUUGCCGAGUAGGUGGAAUGAACCAUAAAC
..(((((((....((((((((.((((.(((.(((......))).).)).))).(((((((...)))))))..........).))))))))...)))))))..((((......)))).... ( -36.60)
>consensus
UAACUUGGCUAUGAAAUUAUGGCACCGUGCCGCCAUAUUCGGUUGUCAGGGUUUCGUUAUUGAGUGGCGACAUAAAUUAAGGCAUGAUUUAUUGCCGAGUAGGUGGAAUGGACCAUAAAC
................((((((..((((.(((((.(((((.(((((((....((((....))))))))))).........((((........)))))))))))))).)))).)))))).. (-35.40 = -34.77 +  -0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:11:11 2006