Locus 1971

Sequence ID	2R_DroMel_CAF1
Location	7,449,072 – 7,449,234
Length	162
Max. P	0.999433

overview

Window 2

Location	7,449,072 – 7,449,178
Length	106
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	89.87
Mean single sequence MFE	-33.22
Consensus MFE	-27.40
Energy contribution	-29.32
Covariance contribution	1.92
Combinations/Pair	1.06
Mean z-score	-1.94
Structure conservation index	0.82
SVM decision value	0.20
SVM RNA-class probability	0.632892
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7449072 106 - 20766785
GCACCUUUGCAGCUCCAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAUUGAGUUGGCUGUGGGGCAGCUGCCCGAACUUA
........((((((((.....(((((((....)))))))(..(((((.(((..(...(((((...)))))...)..))).)))))..))).))))))......... ( -36.40)
>DroSec_CAF1 65506 106 - 1
GCACCUUUGCAGCUCCAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAUUGAGUUGGCUGUGAGGCAGCUGCCCCGACUUA
........((((((((.....(((((((....)))))))..((((((.(((..(...(((((...)))))...)..))).))))))..)).))))))......... ( -33.70)
>DroSim_CAF1 57673 106 - 1
GCACCUUUGCAGCUCCAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAUUGAGUUGGCUGUGGGGCAGCUGCCCCGACUUA
........((((((((.....(((((((....)))))))(..(((((.(((..(...(((((...)))))...)..))).)))))..))).))))))......... ( -36.40)
>DroEre_CAF1 65643 106 - 1
GCACCUUUGCAGCUCCAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAUUGAGUUGGCUGUGGGGCAGCUGCCCCGACUUA
........((((((((.....(((((((....)))))))(..(((((.(((..(...(((((...)))))...)..))).)))))..))).))))))......... ( -36.40)
>DroYak_CAF1 63971 106 - 1
GCACCUUCGCAGCUCUAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAUUGAGUUGGCUGUGGGGCAGCUGCCCCGACUUA
........((((((((.....(((((((....)))))))(..(((((.(((..(...(((((...)))))...)..))).)))))..))).))))))......... ( -34.40)
>DroAna_CAF1 62966 85 - 1
---------------------CCAGCAGCCGUCUGCAGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAUUGAGUUGAAUGUUGGGCAGCUGCCCCAACUUA
---------------------.((((.((((.((((.....)))).)..........((((((((((((......))))))))).)))))).)))).......... ( -22.00)
>consensus
GCACCUUUGCAGCUCCAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAUUGAGUUGGCUGUGGGGCAGCUGCCCCGACUUA
........((((((((.....(((((((....)))))))((((((((.(((..(...(((((...)))))...)..))).)))))))))).))))))......... (-27.40 = -29.32 +   1.92)

alignment

secondary structure

dotplot

Window 3

Location	7,449,104 – 7,449,209
Length	105
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	96.95
Mean single sequence MFE	-33.96
Consensus MFE	-32.86
Energy contribution	-33.26
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.97
SVM decision value	3.17
SVM RNA-class probability	0.998632
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7449104 105 + 20766785
AUUUCAAAUUAAAUUUGUAUUCAAAUAGACCGCAGACGGCAGACGGCUGCCGUUGGAUGGAGCUGCAAAGGUGCUACAGUGGUGCCAUUGGUGGUGCUAUUGUUG
............(((((....)))))...((((.((((((((....)))))))).).)))(((.((....)))))(((((((..(((....)))..))))))).. ( -34.30)
>DroSec_CAF1 65538 105 + 1
AUUUCAAAUUAAAUUUGUAUUCAAAUAGACCGCAGACGGCAGACGGCUGCCGUUGGAUGGAGCUGCAAAGGUGCUACAGUGGUGCCAUUGGUGGUGCUAUUGGUG
............(((((....)))))...((((.((((((((....)))))))).).)))(((.((....))))).((((((..(((....)))..))))))... ( -34.10)
>DroSim_CAF1 57705 105 + 1
AUUUCAAAUUAAAUUUGUAUUCAAAUAGACCGCAGACGGCAGACGGCUGCCGUUGGAUGGAGCUGCAAAGGUGCUACAGUGGUGCCAUUGGUGGUGCUAUUGGUG
............(((((....)))))...((((.((((((((....)))))))).).)))(((.((....))))).((((((..(((....)))..))))))... ( -34.10)
>DroEre_CAF1 65675 104 + 1
AUUUCAAAUUAAAUUUGUAUUCAAAUAGACCGCAGACGGCAGACGGCUGCCGUUGGAUGGAGCUGCAAAGGUGCUACAGUGGUGCCAU-AGUGGUGCUAUUGGUG
............(((((....)))))...((((.((((((((....)))))))).).)))(((.((....))))).((((((..((..-...))..))))))... ( -33.20)
>DroYak_CAF1 64003 104 + 1
AUUUCAAAUUAAAUUUGUAUUCAAAUAGACCGCAGACGGCAGACGGCUGCCGUUGGAUAGAGCUGCGAAGGUGCUACAGAGGUGCCAC-AGUGGUGCUAUUGGUG
............(((((....)))))..(((...((((((((....)))))))).(((((.((..(...((..((.....))..))..-.)..)).)))))))). ( -34.10)
>consensus
AUUUCAAAUUAAAUUUGUAUUCAAAUAGACCGCAGACGGCAGACGGCUGCCGUUGGAUGGAGCUGCAAAGGUGCUACAGUGGUGCCAUUGGUGGUGCUAUUGGUG
............(((((....)))))...((((.((((((((....)))))))).).)))(((.((....))))).((((((..(((....)))..))))))... (-32.86 = -33.26 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	7,449,104 – 7,449,209
Length	105
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	96.95
Mean single sequence MFE	-24.20
Consensus MFE	-22.76
Energy contribution	-22.96
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.74
Structure conservation index	0.94
SVM decision value	2.14
SVM RNA-class probability	0.988879
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7449104 105 - 20766785
CAACAAUAGCACCACCAAUGGCACCACUGUAGCACCUUUGCAGCUCCAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAU
....(((((.(((.....(((.....((((((.....))))))......)))(((((((....)))))))....))))))))......(((((...))))).... ( -23.30)
>DroSec_CAF1 65538 105 - 1
CACCAAUAGCACCACCAAUGGCACCACUGUAGCACCUUUGCAGCUCCAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAU
..(.(((((.(((.....(((.....((((((.....))))))......)))(((((((....)))))))....)))))))).)....(((((...))))).... ( -23.90)
>DroSim_CAF1 57705 105 - 1
CACCAAUAGCACCACCAAUGGCACCACUGUAGCACCUUUGCAGCUCCAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAU
..(.(((((.(((.....(((.....((((((.....))))))......)))(((((((....)))))))....)))))))).)....(((((...))))).... ( -23.90)
>DroEre_CAF1 65675 104 - 1
CACCAAUAGCACCACU-AUGGCACCACUGUAGCACCUUUGCAGCUCCAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAU
..(.(((((.(((.((-((((.....)))))).......((((.........(((((((....))))))))))))))))))).)....(((((...))))).... ( -25.20)
>DroYak_CAF1 64003 104 - 1
CACCAAUAGCACCACU-GUGGCACCUCUGUAGCACCUUCGCAGCUCUAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAU
..(.(((((.(((..(-((.(((....))).))).....((((.........(((((((....))))))))))))))))))).)....(((((...))))).... ( -24.70)
>consensus
CACCAAUAGCACCACCAAUGGCACCACUGUAGCACCUUUGCAGCUCCAUCCAACGGCAGCCGUCUGCCGUCUGCGGUCUAUUUGAAUACAAAUUUAAUUUGAAAU
....(((((.(((.....(((.....((((((.....))))))......)))(((((((....)))))))....))))))))......(((((...))))).... (-22.76 = -22.96 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	7,449,138 – 7,449,234
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	96.66
Mean single sequence MFE	-40.12
Consensus MFE	-40.48
Energy contribution	-40.68
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	1.01
SVM decision value	3.60
SVM RNA-class probability	0.999433
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7449138 96 + 20766785
GACGGCAGACGGCUGCCGUUGGAUGGAGCUGCAAAGGUGCUACAGUGGUGCCAUUGGUGGUGCUAUUGUUGGUGCUGCUCAACCACUCAACUGGGC
((((((((....))))))))((...((((......((..(((((((((..(((....)))..)))))).)))..))))))..)).(((....))). ( -41.20)
>DroSec_CAF1 65572 96 + 1
GACGGCAGACGGCUGCCGUUGGAUGGAGCUGCAAAGGUGCUACAGUGGUGCCAUUGGUGGUGCUAUUGGUGGUGCUGCUCAACCACUCAACUGGGC
((((((((....))))))))((...((((......((..(((((((((..(((....)))..))))).))))..))))))..)).(((....))). ( -41.20)
>DroSim_CAF1 57739 96 + 1
GACGGCAGACGGCUGCCGUUGGAUGGAGCUGCAAAGGUGCUACAGUGGUGCCAUUGGUGGUGCUAUUGGUGGUGCUGCUCAACCACUCAACUGGGC
((((((((....))))))))((...((((......((..(((((((((..(((....)))..))))).))))..))))))..)).(((....))). ( -41.20)
>DroEre_CAF1 65709 95 + 1
GACGGCAGACGGCUGCCGUUGGAUGGAGCUGCAAAGGUGCUACAGUGGUGCCAU-AGUGGUGCUAUUGGUGGUGCUGCUCAACCACUCAACUGGGC
((((((((....))))))))((...((((......((..(((((((((..((..-...))..))))).))))..))))))..)).(((....))). ( -40.30)
>DroYak_CAF1 64037 95 + 1
GACGGCAGACGGCUGCCGUUGGAUAGAGCUGCGAAGGUGCUACAGAGGUGCCAC-AGUGGUGCUAUUGGUGGUGCUGCUCAACCACUCAACUGGGC
((((((((....)))))))).(((((.((..(...((..((.....))..))..-.)..)).)))))((((((........))))))......... ( -36.70)
>consensus
GACGGCAGACGGCUGCCGUUGGAUGGAGCUGCAAAGGUGCUACAGUGGUGCCAUUGGUGGUGCUAUUGGUGGUGCUGCUCAACCACUCAACUGGGC
((((((((....))))))))((...((((......((..(((((((((..(((....)))..)))))).)))..))))))..)).(((....))). (-40.48 = -40.68 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:48 2006