Locus 668

Sequence ID	3R_DroMel_CAF1
Location	2,437,705 – 2,437,964
Length	259
Max. P	0.994585

overview

Window 8

Location	2,437,705 – 2,437,825
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.00
Mean single sequence MFE	-45.04
Consensus MFE	-34.30
Energy contribution	-36.30
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.45
Structure conservation index	0.76
SVM decision value	1.26
SVM RNA-class probability	0.936802
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2437705 120 - 27905053
CGCGUUCGAGAACGGAUGCGGAUGCUGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUUAAAUU
(((((.(((..((((((((((((.(......).))))))))))))..)).(((((.(((((((.......)))))))...((........))))))).).)))))............... ( -43.80)
>DroSec_CAF1 4069 119 - 1
CGCGUUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCC-CCGUGCGUGGGCUUCAAUUAAAUU
(((((..((..((((((((((((.((....)).))))))))))))..))((((((.(((((((.......)))))))...((........)))))-))).)))))............... ( -46.90)
>DroSim_CAF1 4164 120 - 1
CGCGUUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUUAAAUU
(((((.((.....((((((((((((((((....)))))))))))).))))(((((.(((((((.......)))))))...((........))))))))).)))))............... ( -46.30)
>DroEre_CAF1 4152 120 - 1
CGCAUUCGAGUCCGGCUCCGGAUCCGGACUCGGAUCCGCGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUUAAAUU
...(((.((((((((((((((((((((((.((....)).))))).)))))))))))(((((((.......))))))).............((((......)))))))))).)))...... ( -51.20)
>DroYak_CAF1 3767 111 - 1
C---------ACUGGCUCCGGAUUCGGAUUCGGAUCCGUGUUCGUGGUCCGUGCCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUUAAAUU
.---------((.(((..(((((.(((((....))))).)))))..))).))(((((((.((((......((((((...........))))))...))))))).))))............ ( -37.00)
>consensus
CGCGUUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAAGUUAACAAUUACGCCCCCGUGCGUGGGCUUCAAUUAAAUU
.............((((((((((((((((....)))))))))))).))))(((((((((((((.......))))))..............((((......)))))))))))......... (-34.30 = -36.30 +   2.00)

alignment

secondary structure

dotplot

Window 9

Location	2,437,745 – 2,437,862
Length	117
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	90.43
Mean single sequence MFE	-43.22
Consensus MFE	-34.54
Energy contribution	-35.94
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-1.36
Structure conservation index	0.80
SVM decision value	-0.05
SVM RNA-class probability	0.509733
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2437745 117 + 27905053
UUUCAUUACGUAAUAUCCGUAACGGGCCCCGGACCACGAACACGGAUCCGAAUCAGCAUCCGCAUCCGUUCUCGAACGCGGUUCCAGUGGCCUUGGCCUCUUGGGGGAUUAUGGGGU
....((..((((((.(((.(((.(((((..((.((((((..((((((.((..........)).))))))..))((((...))))..))))))..))))).))).)))))))))..)) ( -40.60)
>DroSec_CAF1 4108 117 + 1
UUUCAUUACGUAAUAUCCGUAACGGGCCCCGGACCACGAACACGGAUCCGAAUCCGCAUCCGCAUCCGUUCUCGAACGCGGUUCCAGUGGCCUUGGCCUCUUGGGGGAUUAUGGGGU
....((..((((((.(((.(((.(((((..((.((((((((.(((((.((....)).)))))...(((((....)))).)))))..))))))..))))).))).)))))))))..)) ( -42.00)
>DroSim_CAF1 4204 117 + 1
UUUCAUUACGUAAUAUCCGUAACGGGCCCCGGACCACGAACACGGAUCCGAAUCCGCAUCCGCAUCCGUUCUCGAACGCGGUUCCAGUGGCCUUGGCCUCUUGGGGGAUUAUGGGGU
....((..((((((.(((.(((.(((((..((.((((((((.(((((.((....)).)))))...(((((....)))).)))))..))))))..))))).))).)))))))))..)) ( -42.00)
>DroEre_CAF1 4192 117 + 1
UUUCAUUACGUAAUAUCCGUAACGGGCCCCGGACCACGAACGCGGAUCCGAGUCCGGAUCCGGAGCCGGACUCGAAUGCGGUUCGAGUGGCCUUGGCCUCUUUGGGGAUUAUGGGGU
....((..((((((..(((.((.(((((..((.((((((((.((.((.(((((((((........))))))))).)).))))))..))))))..))))).)))))..))))))..)) ( -52.50)
>DroYak_CAF1 3807 106 + 1
UUUCAUUACGUAAUAUCCGUAACGGGGCACGGACCACGAACACGGAUCCGAAUCCGAAUCCGGAGCCAGU---------G--GCCAGUGGCCUUGGCCUCUUGGGGGAUUAUGGGGU
....((..((((((.(((.(((.(((((..((.((((...(((((.((((..........)))).)).))---------)--....))))))...)))))))).)))))))))..)) ( -39.00)
>consensus
UUUCAUUACGUAAUAUCCGUAACGGGCCCCGGACCACGAACACGGAUCCGAAUCCGCAUCCGCAUCCGUUCUCGAACGCGGUUCCAGUGGCCUUGGCCUCUUGGGGGAUUAUGGGGU
....((..((((((.(((.(((.(((((..((.((((.....(((((.((....)).)))))...((((........)))).....))))))..))))).))).)))))))))..)) (-34.54 = -35.94 +   1.40)

alignment

secondary structure

dotplot

Window 0

Location	2,437,745 – 2,437,862
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	90.43
Mean single sequence MFE	-48.00
Consensus MFE	-37.58
Energy contribution	-40.46
Covariance contribution	2.88
Combinations/Pair	1.03
Mean z-score	-3.10
Structure conservation index	0.78
SVM decision value	2.49
SVM RNA-class probability	0.994585
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2437745 117 - 27905053
ACCCCAUAAUCCCCCAAGAGGCCAAGGCCACUGGAACCGCGUUCGAGAACGGAUGCGGAUGCUGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAA
.((((...........((.(((....))).))(((.(((((.......((((((.(((((....))))).))))))...))))))))))))..(((((((.......)))))))... ( -47.70)
>DroSec_CAF1 4108 117 - 1
ACCCCAUAAUCCCCCAAGAGGCCAAGGCCACUGGAACCGCGUUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAA
.((((..(((((.(((.(.(((....))).))))..(((((((((....)))))))))....))))).(((((((....)).)))))))))..(((((((.......)))))))... ( -51.00)
>DroSim_CAF1 4204 117 - 1
ACCCCAUAAUCCCCCAAGAGGCCAAGGCCACUGGAACCGCGUUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAA
.((((..(((((.(((.(.(((....))).))))..(((((((((....)))))))))....))))).(((((((....)).)))))))))..(((((((.......)))))))... ( -51.00)
>DroEre_CAF1 4192 117 - 1
ACCCCAUAAUCCCCAAAGAGGCCAAGGCCACUCGAACCGCAUUCGAGUCCGGCUCCGGAUCCGGACUCGGAUCCGCGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAA
...................(((....)))(((((((.....)))))))..((((((((((((((((.((....)).))))).)))))))))))(((((((.......)))))))... ( -52.50)
>DroYak_CAF1 3807 106 - 1
ACCCCAUAAUCCCCCAAGAGGCCAAGGCCACUGGC--C---------ACUGGCUCCGGAUUCGGAUUCGGAUCCGUGUUCGUGGUCCGUGCCCCGUUACGGAUAUUACGUAAUGAAA
...................(((....)))((.(((--(---------((..((..((((((((....)))))))).))..)))))).))....(((((((.......)))))))... ( -37.80)
>consensus
ACCCCAUAAUCCCCCAAGAGGCCAAGGCCACUGGAACCGCGUUCGAGAACGGAUGCGGAUGCGGAUUCGGAUCCGUGUUCGUGGUCCGGGGCCCGUUACGGAUAUUACGUAAUGAAA
.((((..(((((.(((.(.(((....))).))))..(((((((((....)))))))))....))))).(((((((....)).)))))))))..(((((((.......)))))))... (-37.58 = -40.46 +   2.88)

alignment

secondary structure

dotplot

Window 1

Location	2,437,862 – 2,437,964
Length	102
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	96.30
Mean single sequence MFE	-26.30
Consensus MFE	-24.50
Energy contribution	-24.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.20
Structure conservation index	0.93
SVM decision value	0.33
SVM RNA-class probability	0.692159
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2437862 102 - 27905053
GGGCAAAGUGCGGAGAUAAAGAGCACCGUGAAUACGAACAAAAA--UAUGCAAGGGGAUGCGUAAUGAAAGCAUUGCAAUUUUUCAGCUUUUUGCCGCCACUUU
....(((((((((...((((((((..(((....)))........--.......(..((...((((((....))))))...))..).))))))))))).)))))) ( -25.70)
>DroSec_CAF1 4225 102 - 1
GGGCAAAGUGCGGAGAUAAAGAGCACCGGGAAUACGAACAAAAA--UAUGCAAGGGGAUGCGUAAUGAAAGCAUUGCAAUUUUUCAGCUUUUUGCCGCCACUUU
....(((((((((...((((((((..((......))........--.......(..((...((((((....))))))...))..).))))))))))).)))))) ( -25.90)
>DroSim_CAF1 4321 102 - 1
GGGCAAAGUGCGGAGAUAAAGAGCACCGGGAAUACGAACAAAAA--UAUGCAAGGGGAUGCGUAAUGAAAGCAUUGCAAUUUUUCAGCUUUUUGCCGCCACUUU
....(((((((((...((((((((..((......))........--.......(..((...((((((....))))))...))..).))))))))))).)))))) ( -25.90)
>DroEre_CAF1 4309 102 - 1
GGGCAAAGUGCGGAGAUAAAGAGCACCGGGAAUACCGACAAAAA--UAUGCAAUGGGAUGCGUAAUGAAAGCAUUGCAAUUUUUCAGCUUUUUGCCGCCACUUU
....(((((((((...((((((((..(((.....)))..(((((--(..(((......)))((((((....)))))).))))))..))))))))))).)))))) ( -28.90)
>DroYak_CAF1 3913 104 - 1
GGGCAAAGUGCGGAGAUAAAGAGCACCGGGAAUAUCGACAACAAUAUAUGCAAUGGGAUGCGUAAUGAAAGCAUUGCAAUUUUUCAGCUUUUUGCCGCCACUUU
....(((((((((...((((((((..(((.....)))................((.(((((.........))))).))........))))))))))).)))))) ( -25.10)
>consensus
GGGCAAAGUGCGGAGAUAAAGAGCACCGGGAAUACGAACAAAAA__UAUGCAAGGGGAUGCGUAAUGAAAGCAUUGCAAUUUUUCAGCUUUUUGCCGCCACUUU
....(((((((((...((((((((.........................(((......)))((((((....)))))).........))))))))))).)))))) (-24.50 = -24.50 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:53 2006