Locus 6520

Sequence ID	3L_DroMel_CAF1
Location	17,271,672 – 17,271,869
Length	197
Max. P	0.999757

overview

Window 4

Location	17,271,672 – 17,271,792
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-29.72
Consensus MFE	-25.10
Energy contribution	-25.30
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.97
Structure conservation index	0.84
SVM decision value	1.14
SVM RNA-class probability	0.921698
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271672 120 + 23771897
UUUCGGAGUUGCCGGGAAAAACUCUGUGAAAAAUAGAGCGCCGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAU
(..(((.....)))..)....((((((.....))))))((((((((.((((((....)))))).....)))))).))...(((.........)))...(((((........))))).... ( -31.10)
>DroSec_CAF1 155188 120 + 1
UUUCGGAGUUGCCGGGAAAAACUCUACGAAAAAUAGAGCGCAGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAU
.....(((((((((..(.....((((.(((....(((((.(((....))).)))))..)))...)))))..)))).....(((.........)))..))))).................. ( -26.40)
>DroSim_CAF1 150221 120 + 1
UUUCGGAGUUGCCGGGAAAAACUCUGCGAAAAAUAGAGCGCAGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAU
(..(((.....)))..).......((((((....(((((.(((....))).)))))..)))....((.(((...(((....)))...))).)))))..(((((........))))).... ( -29.10)
>DroEre_CAF1 158032 120 + 1
UUUCGGAGUUGCCGGGGAAAACUCUGGGAAAAAUAGAGCGCAGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAU
..((((((((.((((((....))))))(((....(((((.(((....))).)))))..))).....))))))))......(((.........)))...(((((........))))).... ( -32.00)
>DroYak_CAF1 162840 120 + 1
UUUCGGAGUUGCCGGCGAAAACUCGGUGAAAAAUAGAGCGCAGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAU
.....(((((..((((((((.((...((((....(((((.(((....))).)))))..))))...)).))))).(((....))).......)))...))))).................. ( -30.00)
>consensus
UUUCGGAGUUGCCGGGAAAAACUCUGCGAAAAAUAGAGCGCAGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAU
.....(((((..(((............(((....(((((.(((....))).)))))..)))......((((((........))))))....)))...))))).................. (-25.10 = -25.30 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	17,271,712 – 17,271,832
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.17
Mean single sequence MFE	-32.50
Consensus MFE	-31.60
Energy contribution	-31.36
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-2.14
Structure conservation index	0.97
SVM decision value	2.75
SVM RNA-class probability	0.996770
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271712 120 + 23771897
CCGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUCAGCACUCCUGCCUUU
((((((.((((((....)))))).....))))))(((....))).....((((((((.(((((........)))))...))))))))((((((......)))))).(((....))).... ( -35.50)
>DroSec_CAF1 155228 120 + 1
CAGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUCAGCACUCCUGCCUUU
..((((.((((((....)))))).....))))(((.(...((.......((((((((.(((((........)))))...))))))))((((((......)))))).))....).)))... ( -32.30)
>DroSim_CAF1 150261 120 + 1
CAGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUCAGCACUCCUGCCUUU
..((((.((((((....)))))).....))))(((.(...((.......((((((((.(((((........)))))...))))))))((((((......)))))).))....).)))... ( -32.30)
>DroEre_CAF1 158072 120 + 1
CAGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUUAGCACUCCUGCCUUU
...((((((.(((.(((..........((((((........))))))..((((((((.(((((........)))))...)))))))).)))..)))...)))))).(((....))).... ( -31.20)
>DroYak_CAF1 162880 120 + 1
CAGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUUAGCACUCCUGCCUUU
...((((((.(((.(((..........((((((........))))))..((((((((.(((((........)))))...)))))))).)))..)))...)))))).(((....))).... ( -31.20)
>consensus
CAGAAAGUUGGGCUCUUGUUCAAAUGGAUUUCGGUCGUAAGCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUCAGCACUCCUGCCUUU
..((((.((((((....)))))).....))))(((.(...((.......((((((((.(((((........)))))...))))))))((((((......)))))).))....).)))... (-31.60 = -31.36 +  -0.24)

alignment

secondary structure

dotplot

Window 6

Location	17,271,712 – 17,271,832
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.17
Mean single sequence MFE	-33.10
Consensus MFE	-33.00
Energy contribution	-32.76
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-2.60
Structure conservation index	1.00
SVM decision value	3.77
SVM RNA-class probability	0.999603
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271712 120 - 23771897
AAAGGCAGGAGUGCUGAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGCUUACGACCGAAAUCCAUUUGAACAAGAGCCCAACUUUCGG
..((((.(((((((..(.....)..)).)))))((((((((...(((((........))))).)))))))).......))))....((((((....(((.....))).......)))))) ( -33.30)
>DroSec_CAF1 155228 120 - 1
AAAGGCAGGAGUGCUGAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGCUUACGACCGAAAUCCAUUUGAACAAGAGCCCAACUUUCUG
...(((.(((((((..(.....)..)).)))))((((((((...(((((........))))).))))))))..((((((........))))))..............))).......... ( -32.80)
>DroSim_CAF1 150261 120 - 1
AAAGGCAGGAGUGCUGAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGCUUACGACCGAAAUCCAUUUGAACAAGAGCCCAACUUUCUG
...(((.(((((((..(.....)..)).)))))((((((((...(((((........))))).))))))))..((((((........))))))..............))).......... ( -32.80)
>DroEre_CAF1 158072 120 - 1
AAAGGCAGGAGUGCUAAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGCUUACGACCGAAAUCCAUUUGAACAAGAGCCCAACUUUCUG
...(((.((((((((((.....))))).)))))((((((((...(((((........))))).))))))))..((((((........))))))..............))).......... ( -33.30)
>DroYak_CAF1 162880 120 - 1
AAAGGCAGGAGUGCUAAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGCUUACGACCGAAAUCCAUUUGAACAAGAGCCCAACUUUCUG
...(((.((((((((((.....))))).)))))((((((((...(((((........))))).))))))))..((((((........))))))..............))).......... ( -33.30)
>consensus
AAAGGCAGGAGUGCUGAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGCUUACGACCGAAAUCCAUUUGAACAAGAGCCCAACUUUCUG
...(((.((((((((((.....))))).)))))((((((((...(((((........))))).))))))))..((((((........))))))..............))).......... (-33.00 = -32.76 +  -0.24)

alignment

secondary structure

dotplot

Window 7

Location	17,271,752 – 17,271,869
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.97
Mean single sequence MFE	-34.34
Consensus MFE	-32.32
Energy contribution	-32.08
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-2.58
Structure conservation index	0.94
SVM decision value	3.71
SVM RNA-class probability	0.999552
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271752 117 + 23771897
GCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUCAGCACUCCUGCCUUU-UUUGGAAUGUGUGGUUUUC--GUUUUGCUUGGCCACAUC
((((((((((((((((..(((((........)))))........(((((((((......)))))))))..(((.......-...)))...))))))))).--)))))))........... ( -34.40)
>DroSec_CAF1 155268 117 + 1
GCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUCAGCACUCCUGCCUUU-UUUGGAAUGUGUGGUUUUC--GUUUUGCUUGGCCACAUC
((((((((((((((((..(((((........)))))........(((((((((......)))))))))..(((.......-...)))...))))))))).--)))))))........... ( -34.40)
>DroSim_CAF1 150301 117 + 1
GCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUCAGCACUCCUGCCUUU-UUUGGAAUGUGUGGUUUUC--GUUUUGCUUGGCCACAUC
((((((((((((((((..(((((........)))))........(((((((((......)))))))))..(((.......-...)))...))))))))).--)))))))........... ( -34.40)
>DroEre_CAF1 158112 117 + 1
GCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUUAGCACUCCUGCCUUU-UUUGGAAUGUGUGGUUUUU--GUUUUGCUUGGCCACAUC
(((((((((((((((((.(((((........)))))...)))))))(((((((......)))))))((((.....((...-...))...))))....)))--)))))))........... ( -33.00)
>DroYak_CAF1 162920 120 + 1
GCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUUAGCACUCCUGCCUUUUUUUGGAAUGUGUGGUUUUUGUGUUUUGCUUGGCCACAUC
((((((((.((((((((.(((((........)))))...))))))))........((((((((...(((.(((...........))).)))..))))))))))))))))........... ( -35.50)
>consensus
GCGAAAUAAAACCGCAAAACUCAAAAUGAAAUGAGUAAAUUGCGGUUGAAGUUGCCAAAAGCUUCAGCACUCCUGCCUUU_UUUGGAAUGUGUGGUUUUC__GUUUUGCUUGGCCACAUC
((.......((((((((.(((((........)))))...))))))))((((((......)))))).))..(((...........)))..((((((((..............)))))))). (-32.32 = -32.08 +  -0.24)

alignment

secondary structure

dotplot

Window 8

Location	17,271,752 – 17,271,869
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.97
Mean single sequence MFE	-32.41
Consensus MFE	-30.57
Energy contribution	-30.33
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-2.80
Structure conservation index	0.94
SVM decision value	4.01
SVM RNA-class probability	0.999757
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17271752 117 - 23771897
GAUGUGGCCAAGCAAAAC--GAAAACCACACAUUCCAAA-AAAGGCAGGAGUGCUGAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGC
((.((.(((((((.....--(.....).((((((((...-.......)))))).))..)))..)))).)).))((((((((...(((((........))))).))))))))......... ( -33.40)
>DroSec_CAF1 155268 117 - 1
GAUGUGGCCAAGCAAAAC--GAAAACCACACAUUCCAAA-AAAGGCAGGAGUGCUGAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGC
((.((.(((((((.....--(.....).((((((((...-.......)))))).))..)))..)))).)).))((((((((...(((((........))))).))))))))......... ( -33.40)
>DroSim_CAF1 150301 117 - 1
GAUGUGGCCAAGCAAAAC--GAAAACCACACAUUCCAAA-AAAGGCAGGAGUGCUGAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGC
((.((.(((((((.....--(.....).((((((((...-.......)))))).))..)))..)))).)).))((((((((...(((((........))))).))))))))......... ( -33.40)
>DroEre_CAF1 158112 117 - 1
GAUGUGGCCAAGCAAAAC--AAAAACCACACAUUCCAAA-AAAGGCAGGAGUGCUAAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGC
..(((((...........--.....))))).........-....((.((((((((((.....))))).)))))((((((((...(((((........))))).)))))))).......)) ( -30.99)
>DroYak_CAF1 162920 120 - 1
GAUGUGGCCAAGCAAAACACAAAAACCACACAUUCCAAAAAAAGGCAGGAGUGCUAAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGC
..(((((..................)))))..............((.((((((((((.....))))).)))))((((((((...(((((........))))).)))))))).......)) ( -30.87)
>consensus
GAUGUGGCCAAGCAAAAC__GAAAACCACACAUUCCAAA_AAAGGCAGGAGUGCUGAAGCUUUUGGCAACUUCAACCGCAAUUUACUCAUUUCAUUUUGAGUUUUGCGGUUUUAUUUCGC
..(((((..................)))))..............((.((((((((((.....))))).)))))((((((((...(((((........))))).)))))))).......)) (-30.57 = -30.33 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:35 2006