Locus 4224

Sequence ID	2L_DroMel_CAF1
Location	12,091,458 – 12,091,587
Length	129
Max. P	0.886842

overview

Window 7

Location	12,091,458 – 12,091,553
Length	95
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	80.59
Mean single sequence MFE	-21.95
Consensus MFE	-15.38
Energy contribution	-15.18
Covariance contribution	-0.19
Combinations/Pair	1.11
Mean z-score	-2.13
Structure conservation index	0.70
SVM decision value	0.94
SVM RNA-class probability	0.886842
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12091458 95 + 22407834
CCAGGAAUGACUGGGAGCCUUGUAAUCGCAAUUACCAUGGCCAAAAUAUCAAAAGAUA------------AUGCCAUCCUGGCCAGACACAAAAAU---AUGUCGAAACA
((((((.....((((.(((..(((((....)))))...))))....((((....))))------------...)))))))))...((((.......---.))))...... ( -21.70)
>DroSec_CAF1 27871 95 + 1
CCAGGAACGACUGGCAGCCUUGUAAUCGCAAUUACCAUGGCCAAAAUAUCAAAAGAUA------------AUACCAUCCUGGCCAGACACAAAAAU---AUGUCGAAACA
((((((.....(((..(((..(((((....)))))...))).....((((....))))------------...)))))))))...((((.......---.))))...... ( -20.90)
>DroSim_CAF1 28163 95 + 1
CCAGGAACGACUGGCAGCCUUGUAAUCGCAAUUACCAUGGCCAAAAUAUCAAAAGAUA------------AUGCCAUCCUGGCCAGACACAAAAAU---AUGUCGAAACA
((((((.....((((((((..(((((....)))))...))).....((((....))))------------.)))))))))))...((((.......---.))))...... ( -26.10)
>DroEre_CAF1 28206 93 + 1
CCAGGAACGACUGUCGGCCUUGUAAUCGCAAUUAUCAUGGCCAAAAUAUCAAAAGAUA------------ACGCAAUCCUGGCCAGACA--AAAAC---AUGCCGAAACA
((((((.((......((((.((((((....)))).)).))))....((((....))))------------.))...)))))).......--.....---........... ( -20.20)
>DroYak_CAF1 29954 94 + 1
CCAGGAACGUCUGCCAGCCUUGUAAUCGCAAUUACCAUGGCCAAAAUAUCAAAAGAUA------------AUGCAAUCCUGGCCAGACAG-AAAAC---AUCUCGAAACA
........(((((((((..(((((...((..........)).....((((....))))------------.)))))..)))).)))))..-.....---........... ( -19.50)
>DroAna_CAF1 29533 110 + 1
CCAGGAAGAGCUGCUGGCUCUGUAAUCGCAAUUAUCACGGCACGAAUAUCAAAAGACAGCGUUUAACAUGACAUGAUCCUGGCGAGAUUGGGAAACGCCAUUUUUUAUUA
((((((...((((((.(((.((((((....)))).)).)))..(.....)...)).))))(((......)))....)))))).((((.(((......))).))))..... ( -23.30)
>consensus
CCAGGAACGACUGGCAGCCUUGUAAUCGCAAUUACCAUGGCCAAAAUAUCAAAAGAUA____________AUGCCAUCCUGGCCAGACACAAAAAC___AUGUCGAAACA
((((((..........(((..(((((....)))))...))).....((((....))))..................))))))............................ (-15.38 = -15.18 +  -0.19)

alignment

secondary structure

dotplot

Window 8

Location	12,091,458 – 12,091,553
Length	95
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	80.59
Mean single sequence MFE	-27.95
Consensus MFE	-16.30
Energy contribution	-16.38
Covariance contribution	0.08
Combinations/Pair	1.10
Mean z-score	-2.04
Structure conservation index	0.58
SVM decision value	0.38
SVM RNA-class probability	0.713302
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12091458 95 - 22407834
UGUUUCGACAU---AUUUUUGUGUCUGGCCAGGAUGGCAU------------UAUCUUUUGAUAUUUUGGCCAUGGUAAUUGCGAUUACAAGGCUCCCAGUCAUUCCUGG
......(((((---(....))))))...((((((((((..------------((((....))))....((((...(((((....)))))..))))....)))).)))))) ( -29.50)
>DroSec_CAF1 27871 95 - 1
UGUUUCGACAU---AUUUUUGUGUCUGGCCAGGAUGGUAU------------UAUCUUUUGAUAUUUUGGCCAUGGUAAUUGCGAUUACAAGGCUGCCAGUCGUUCCUGG
......(((((---(....))))))...((((((((((..------------((((....))))....((((...(((((....)))))..)))))))).....)))))) ( -28.10)
>DroSim_CAF1 28163 95 - 1
UGUUUCGACAU---AUUUUUGUGUCUGGCCAGGAUGGCAU------------UAUCUUUUGAUAUUUUGGCCAUGGUAAUUGCGAUUACAAGGCUGCCAGUCGUUCCUGG
......(((((---(....))))))...((((((((((..------------((((....))))....((((...(((((....)))))..)))))))).....)))))) ( -30.30)
>DroEre_CAF1 28206 93 - 1
UGUUUCGGCAU---GUUUU--UGUCUGGCCAGGAUUGCGU------------UAUCUUUUGAUAUUUUGGCCAUGAUAAUUGCGAUUACAAGGCCGACAGUCGUUCCUGG
....(((((.(---((..(--((((((((((((((..((.------------.......))..)))))))))).)))))..)))........)))))(((......))). ( -28.30)
>DroYak_CAF1 29954 94 - 1
UGUUUCGAGAU---GUUUU-CUGUCUGGCCAGGAUUGCAU------------UAUCUUUUGAUAUUUUGGCCAUGGUAAUUGCGAUUACAAGGCUGGCAGACGUUCCUGG
......(..((---(((((-(.(((((((((((((..((.------------.......))..)))))))))...(((((....))))).)))).)).))))))..)... ( -25.30)
>DroAna_CAF1 29533 110 - 1
UAAUAAAAAAUGGCGUUUCCCAAUCUCGCCAGGAUCAUGUCAUGUUAAACGCUGUCUUUUGAUAUUCGUGCCGUGAUAAUUGCGAUUACAGAGCCAGCAGCUCUUCCUGG
..........(((......)))......((((((...(((((((....(((.((((....))))..)))..)))))))...........(((((.....))))))))))) ( -26.20)
>consensus
UGUUUCGACAU___AUUUUUGUGUCUGGCCAGGAUGGCAU____________UAUCUUUUGAUAUUUUGGCCAUGGUAAUUGCGAUUACAAGGCUGCCAGUCGUUCCUGG
............................((((((..................((((....))))....((((.((.((((....)))))).)))).........)))))) (-16.30 = -16.38 +   0.08)

alignment

secondary structure

dotplot

Window 9

Location	12,091,497 – 12,091,587
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	79.64
Mean single sequence MFE	-17.92
Consensus MFE	-14.12
Energy contribution	-14.28
Covariance contribution	0.16
Combinations/Pair	1.23
Mean z-score	-1.65
Structure conservation index	0.79
SVM decision value	0.66
SVM RNA-class probability	0.816162
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12091497 90 - 22407834
AUUCAAGUAUCACAAAAUAUAAGAUAUUUAUAUAUGUUUCGACAUAUUUUUGUGUCUGGCCAGGAUGGCAUUAUCUUUUGAUAUUUUGGC
............((((((((((((((..............((((((....))))))..(((.....)))..))))))...)))))))).. ( -20.10)
>DroSec_CAF1 27910 87 - 1
AAUCAAAUAUAAGAUA---UAAGAUAAUUAUAUAUGUUUCGACAUAUUUUUGUGUCUGGCCAGGAUGGUAUUAUCUUUUGAUAUUUUGGC
...........(((((---(((((.......((((((....)))))))))))))))).(((((((((.((........)).))))))))) ( -17.81)
>DroSim_CAF1 28202 90 - 1
AAUCAAAUAUAAGAUAUUAUAAGAUAUUUAUAUAUGUUUCGACAUAUUUUUGUGUCUGGCCAGGAUGGCAUUAUCUUUUGAUAUUUUGGC
.........((((((((((.((((((..............((((((....))))))..(((.....)))..)))))).)))))))))).. ( -22.90)
>DroEre_CAF1 28245 78 - 1
AGCGG----------AGUAUAAGAUGUGUAUAUAUGUUUCGGCAUGUUUU--UGUCUGGCCAGGAUUGCGUUAUCUUUUGAUAUUUUGGC
..(((----------(....(((((((((............)))))))))--..))))((((((((..((........))..)))))))) ( -15.00)
>DroYak_CAF1 29993 79 - 1
AACCG----------AAUCAAUGAUCUGCAUAUAUGUUUCGAGAUGUUUU-CUGUCUGGCCAGGAUUGCAUUAUCUUUUGAUAUUUUGGC
..(((----------((((((.(((.((((....((...(.((((.....-..)))).).))....))))..)))..)))))...)))). ( -13.80)
>consensus
AAUCAA_UAU_A_A_AAUAUAAGAUAUUUAUAUAUGUUUCGACAUAUUUUUGUGUCUGGCCAGGAUGGCAUUAUCUUUUGAUAUUUUGGC
.....................(((((.....((((((....)))))).....))))).(((((((((.((........)).))))))))) (-14.12 = -14.28 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:45 2006