Locus 2381

Sequence ID	X_DroMel_CAF1
Location	6,350,618 – 6,350,766
Length	148
Max. P	0.930110

overview

Window 3

Location	6,350,618 – 6,350,728
Length	110
Sequences	3
Columns	115
Reading direction	forward
Mean pairwise identity	81.76
Mean single sequence MFE	-23.60
Consensus MFE	-15.45
Energy contribution	-16.57
Covariance contribution	1.11
Combinations/Pair	1.04
Mean z-score	-2.25
Structure conservation index	0.65
SVM decision value	0.77
SVM RNA-class probability	0.847378
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6350618 110 + 22224390
AUUAUAAUUAUACUAAUCAAUUCCACAACUUAGUGCACCCGAGCGCAAAGUUGUACAAUUUUGUGAGAGCCCUGAGGGACUUUUAGUCCUUUUUUGUU-----UUUUUUUUUUGC
........................(((((((.((((......)))).))))))).(((......((((((...(((((((.....)))))))...)))-----))).....))). ( -26.30)
>DroSec_CAF1 34619 115 + 1
AUUAUAAUUAUACUAAUCAAUUCCACAACUUAGUGCACCCGAGCGCAAAGUUGUACAAUUUUGUGAGAGCCCUGAGGGACUUUUAGUCCUUUUUCUUUUUUUCUUUUUUUUUUGU
........................(((((((.((((......)))).)))))))((((......(((((....(((((((.....)))))))........)))))......)))) ( -24.40)
>DroEre_CAF1 32799 93 + 1
AUUAUAAUUUUACUAAUCAAUUCCAAAACUUAGGGCACCCGAGCGCAAAGUUGUACAAUUUUGUGAGAGCCUUG-GGUAC-UUUAGUCCCUUAUU--------------------
.............................((((((.((((((((((((((((....))))))))).....))))-))).)-))))).........-------------------- ( -20.10)
>consensus
AUUAUAAUUAUACUAAUCAAUUCCACAACUUAGUGCACCCGAGCGCAAAGUUGUACAAUUUUGUGAGAGCCCUGAGGGACUUUUAGUCCUUUUUU_UU_____UUUUUUUUUUG_
............((...(((....(((((((.((((......)))).)))))))......)))..))......(((((((.....)))))))....................... (-15.45 = -16.57 +   1.11)

alignment

secondary structure

dotplot

Window 4

Location	6,350,618 – 6,350,728
Length	110
Sequences	3
Columns	115
Reading direction	reverse
Mean pairwise identity	81.76
Mean single sequence MFE	-22.32
Consensus MFE	-18.77
Energy contribution	-19.77
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.84
SVM decision value	1.20
SVM RNA-class probability	0.930110
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6350618 110 - 22224390
GCAAAAAAAAAA-----AACAAAAAAGGACUAAAAGUCCCUCAGGGCUCUCACAAAAUUGUACAACUUUGCGCUCGGGUGCACUAAGUUGUGGAAUUGAUUAGUAUAAUUAUAAU
............-----...........(((((.(((((....))))).......((((.(((((((((((((....)))))..)))))))).))))..)))))........... ( -24.80)
>DroSec_CAF1 34619 115 - 1
ACAAAAAAAAAAGAAAAAAAGAAAAAGGACUAAAAGUCCCUCAGGGCUCUCACAAAAUUGUACAACUUUGCGCUCGGGUGCACUAAGUUGUGGAAUUGAUUAGUAUAAUUAUAAU
............................(((((.(((((....))))).......((((.(((((((((((((....)))))..)))))))).))))..)))))........... ( -24.80)
>DroEre_CAF1 32799 93 - 1
--------------------AAUAAGGGACUAAA-GUACC-CAAGGCUCUCACAAAAUUGUACAACUUUGCGCUCGGGUGCCCUAAGUUUUGGAAUUGAUUAGUAAAAUUAUAAU
--------------------.((((...(((((.-(((((-(.((((......................)).)).))))))((........))......)))))....))))... ( -17.35)
>consensus
_CAAAAAAAAAA_____AA_AAAAAAGGACUAAAAGUCCCUCAGGGCUCUCACAAAAUUGUACAACUUUGCGCUCGGGUGCACUAAGUUGUGGAAUUGAUUAGUAUAAUUAUAAU
............................(((((..((((....))))........((((.((((((((.((((....))))...)))))))).))))..)))))........... (-18.77 = -19.77 +   1.00)

alignment

secondary structure

dotplot

Window 5

Location	6,350,653 – 6,350,766
Length	113
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	79.04
Mean single sequence MFE	-30.77
Consensus MFE	-23.99
Energy contribution	-24.43
Covariance contribution	0.45
Combinations/Pair	1.04
Mean z-score	-1.31
Structure conservation index	0.78
SVM decision value	0.12
SVM RNA-class probability	0.593091
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6350653 113 + 22224390
CACCCGAGCGCAAAGUUGUACAAUUUUGUGAGAGCCCUGAGGGACUUUUAGUCCUUUUUUGUU-----UUUUUUUUUUGCCAAGUGGAAAGGGUGGAAA--AGCAGGCACUGACUGAUUU
(((((...(((((((((....)))))))))(((((...(((((((.....)))))))...)))-----))...((((..(...)..)))))))))....--..(((.......))).... ( -31.50)
>DroSec_CAF1 34654 118 + 1
CACCCGAGCGCAAAGUUGUACAAUUUUGUGAGAGCCCUGAGGGACUUUUAGUCCUUUUUCUUUUUUUCUUUUUUUUUUGUGAAGUGGAAAGGGUGGAAA--AGCAGGCACUGACUGAUUU
(((((...(((((((((....)))))))))((((....(((((((.....)))))))..)))).(((((.((((......)))).))))))))))....--..(((.......))).... ( -31.00)
>DroEre_CAF1 32834 96 + 1
CACCCGAGCGCAAAGUUGUACAAUUUUGUGAGAGCCUUG-GGUAC-UUUAGUCCCUUAUU--------------------CAAAUUG--AGGGUGGAAGGCACCAGGCACUGACUGAUUU
........(((((((((....)))))))))((.((((.(-(...(-(((...((((((..--------------------.....))--))))..))))...)))))).))......... ( -29.80)
>consensus
CACCCGAGCGCAAAGUUGUACAAUUUUGUGAGAGCCCUGAGGGACUUUUAGUCCUUUUUU_UU_____UUUUUUUUUUG_CAAGUGGAAAGGGUGGAAA__AGCAGGCACUGACUGAUUU
(((((...(((((((((....)))))))))........(((((((.....))))))).................................)))))........(((.......))).... (-23.99 = -24.43 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:09 2006