Locus 7504

Sequence ID	3L_DroMel_CAF1
Location	20,167,419 – 20,167,571
Length	152
Max. P	0.998386

overview

Window 3

Location	20,167,419 – 20,167,538
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	95.50
Mean single sequence MFE	-30.00
Consensus MFE	-27.50
Energy contribution	-27.90
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.09
Structure conservation index	0.92
SVM decision value	3.09
SVM RNA-class probability	0.998386
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20167419 119 - 23771897
AAGACACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUAGAGUCUAUAGUCUUGGACAAUGCAAGUGCAUGCCAUGUAAAUAGCUAUACAGAUAGCUAUAGCCGCGCAUUAUAUCGUA
...........((((.(((((.(((.....(((((((((..........))))))))).((((....)))))))......((((((((....))))))))....))))).))))..... ( -30.40)
>DroSec_CAF1 4489 117 - 1
AAGACACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUAAGGUCUAU--UCUUGGACUAUGCAAGUGCAUGCCAUGUAAAUAGCUAUACUGAUAGCUAUAGCCGCGCAUUAUAUCGUA
...........((((.(((((.(((...((((((((((..........--))))))))))(((....))).)))......((((((((....))))))))....))))).))))..... ( -30.20)
>DroSim_CAF1 6834 117 - 1
AAGACACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUAAGGUCUAU--UCUUGGACUAUGCAAGUGCAUGCCAUGUAAAUAGCUAUACUGAUAGCUAUAGCCGCGCAUUAUAUCGUA
...........((((.(((((.(((...((((((((((..........--))))))))))(((....))).)))......((((((((....))))))))....))))).))))..... ( -30.20)
>DroEre_CAF1 4514 117 - 1
AAGUCACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUACAGUCUAU--UCUUGGACUAUGCAAGUGCAUGCCAUGUAAAUAGCUAUACAAAUAGCUAUAGCUGCGCAUUAUAUCGUA
...........((((.(((((((((...((((((((((..........--))))))))))(((....))).)))......((((((((....))))))))...)))))).))))..... ( -31.00)
>DroYak_CAF1 4477 117 - 1
AAGACACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUAAAGUCUAU--UCUCGGACUAUGCAAGUGCAUGCCAUGUAAAUAGCUAUACAAAUAGCUAUAGCCGCGCAUUAUAUCAUA
...........((((.(((((.(((...(((((..(((..........--)))..)))))(((....))).)))......((((((((....))))))))....))))).))))..... ( -28.20)
>consensus
AAGACACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUAAAGUCUAU__UCUUGGACUAUGCAAGUGCAUGCCAUGUAAAUAGCUAUACAGAUAGCUAUAGCCGCGCAUUAUAUCGUA
...........((((.(((((.(((....(((((((((............)))))))))((((....)))))))......((((((((....))))))))....))))).))))..... (-27.50 = -27.90 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	20,167,459 – 20,167,571
Length	112
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	96.66
Mean single sequence MFE	-24.48
Consensus MFE	-22.20
Energy contribution	-22.44
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.32
Structure conservation index	0.91
SVM decision value	0.50
SVM RNA-class probability	0.758997
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20167459 112 + 23771897
UACAUGGCAUGCACUUGCAUUGUCCAAGACUAUAGACUCUAUCUUAAACUAAAGGCCUACACAGUACAAUAUGUGUCUUGCACUAAAACUAAGCUGUUGCGUGUCUUCUGGU
.....((((((((...((...(((..........)))...............((((..(((((........)))))...)).))........))...))))))))....... ( -21.20)
>DroSec_CAF1 4529 110 + 1
UACAUGGCAUGCACUUGCAUAGUCCAAGA--AUAGACCUUAUCUUAAACUAAAGGCCUACACAGUACAAUAUGUGUCUUGCACUAAAACUAAGCUUUUGCGUGUCUUCUGGU
.....((((((((((((..((((.(((((--.(((.((((...........)))).)))((((........))))))))).))))....))))....))))))))....... ( -25.50)
>DroSim_CAF1 6874 110 + 1
UACAUGGCAUGCACUUGCAUAGUCCAAGA--AUAGACCUUAUCUUAAACUAAAGGCCUACACAGUACAAUAUGUGUCUUGCACUAAAACUAAGCUUUUGCGUGUCUUCUGGU
.....((((((((((((..((((.(((((--.(((.((((...........)))).)))((((........))))))))).))))....))))....))))))))....... ( -25.50)
>DroEre_CAF1 4554 110 + 1
UACAUGGCAUGCACUUGCAUAGUCCAAGA--AUAGACUGUAUCUUAAACUAAAGGCCUACACAGUACAAUAUGUGACUUGCACUAAAACUAAGCUUUUGCGUGUCUUCUGGU
.....((((((((...((((((((.....--...))))))............((((...((((........))))....)).))........))...))))))))....... ( -24.00)
>DroYak_CAF1 4517 110 + 1
UACAUGGCAUGCACUUGCAUAGUCCGAGA--AUAGACUUUAUCUUAAACUAAAGGCCUACACAGUACAAUAUGUGUCUUGCACUAAAACUAAGCUUUUGCGUGUCUUCUGGU
.....((((((((...((.((((...((.--.....(((((........)))))((..(((((........)))))...)).))...)))).))...))))))))....... ( -26.20)
>consensus
UACAUGGCAUGCACUUGCAUAGUCCAAGA__AUAGACUUUAUCUUAAACUAAAGGCCUACACAGUACAAUAUGUGUCUUGCACUAAAACUAAGCUUUUGCGUGUCUUCUGGU
.....((((((((...((.((((..((((............))))..)))).((((..(((((........)))))...)).))........))...))))))))....... (-22.20 = -22.44 +   0.24)

alignment

secondary structure

dotplot

Window 5

Location	20,167,459 – 20,167,571
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	96.66
Mean single sequence MFE	-27.56
Consensus MFE	-24.66
Energy contribution	-25.06
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.40
Structure conservation index	0.89
SVM decision value	0.63
SVM RNA-class probability	0.806413
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20167459 112 - 23771897
ACCAGAAGACACGCAACAGCUUAGUUUUAGUGCAAGACACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUAGAGUCUAUAGUCUUGGACAAUGCAAGUGCAUGCCAUGUA
........((((((....))........(((((((........))))))))))).(((.....(((((((((..........))))))))).((((....)))))))..... ( -27.50)
>DroSec_CAF1 4529 110 - 1
ACCAGAAGACACGCAAAAGCUUAGUUUUAGUGCAAGACACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUAAGGUCUAU--UCUUGGACUAUGCAAGUGCAUGCCAUGUA
........(((.(((...((((.((..((((.(((((((((........))))((((((((...........)))))))).--))))).)))).))))))...)))..))). ( -28.80)
>DroSim_CAF1 6874 110 - 1
ACCAGAAGACACGCAAAAGCUUAGUUUUAGUGCAAGACACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUAAGGUCUAU--UCUUGGACUAUGCAAGUGCAUGCCAUGUA
........(((.(((...((((.((..((((.(((((((((........))))((((((((...........)))))))).--))))).)))).))))))...)))..))). ( -28.80)
>DroEre_CAF1 4554 110 - 1
ACCAGAAGACACGCAAAAGCUUAGUUUUAGUGCAAGUCACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUACAGUCUAU--UCUUGGACUAUGCAAGUGCAUGCCAUGUA
........((((((....))........(((((((........))))))))))).(((...((((((((((..........--))))))))))(((....))).)))..... ( -27.30)
>DroYak_CAF1 4517 110 - 1
ACCAGAAGACACGCAAAAGCUUAGUUUUAGUGCAAGACACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUAAAGUCUAU--UCUCGGACUAUGCAAGUGCAUGCCAUGUA
........((((((....))........(((((((........))))))))))).(((...(((((..(((..........--)))..)))))(((....))).)))..... ( -25.40)
>consensus
ACCAGAAGACACGCAAAAGCUUAGUUUUAGUGCAAGACACAUAUUGUACUGUGUAGGCCUUUAGUUUAAGAUAAAGUCUAU__UCUUGGACUAUGCAAGUGCAUGCCAUGUA
........((((((....))........(((((((........))))))))))).(((....(((((((((............)))))))))((((....)))))))..... (-24.66 = -25.06 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:57 2006