Locus 7907

Sequence ID	X_DroMel_CAF1
Location	19,696,641 – 19,696,784
Length	143
Max. P	0.949801

overview

Window 2

Location	19,696,641 – 19,696,759
Length	118
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	87.63
Mean single sequence MFE	-54.37
Consensus MFE	-42.46
Energy contribution	-43.63
Covariance contribution	1.17
Combinations/Pair	1.17
Mean z-score	-2.86
Structure conservation index	0.78
SVM decision value	0.59
SVM RNA-class probability	0.790760
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19696641 118 + 22224390
CGGCUGGCAAAAAGCAGGCCGUACAAAGGGUUCAGCUUGGCCGCCUCGCCAAGAUCAAGCUGGGCGAGACGCAGGCCCUCCCUCAAGUGCUGCAGGCACCACUGCAAUGCCCUGAAGG
(((((.((.....)).))))).....(((((...((..((((((((((((.((......)).))))))..)).)))).........((((.....))))....))...)))))..... ( -45.10)
>DroSec_CAF1 3122 118 + 1
CGGCUGGCAAAAAGCAGGCCAUACAAAGGGUUCAGCUUGGCCGCCUCGCCAAGAUCAAGCUGGGCGAGGCGCAGGCCUUCCCUCAGGUGCUGCAGGCACCACUGCAGUGCCCUGAAGG
.(((((((...((((.((((........))))..)))).)))((((((((.((......)).))))))))...))))..((.(((((..((((((......))))))..).)))).)) ( -60.30)
>DroSim_CAF1 2292 118 + 1
CGGCUGGCAAAAAGCAGGCCAUACAAAGGGUUCAGCUUGGCCGCCUCGCCAAGAUCAAGCUGGGCGAGGCGCAGGCCCUCCCUCAGGUGCUGCAGGCACCACUGCAGUGCCCUGAAGG
.((((.((.....)).)))).......(((....(((((..(((((((((.((......)).))))))))))))))...)))(((((..((((((......))))))..).))))... ( -60.20)
>DroEre_CAF1 3392 118 + 1
CGGCUGGCAAAAAGCAGGCCGUACAAAGGGUUCAGCUUGGCCGCCUCGCCCAGAUCCAGCUGGGCGAGGCACAAGCCCUCCUUCAAGUGCUGCAGGCACCACUGCAGUGCCCUGAAGG
.(((((((...((((.((((........))))..)))).)))(((((((((((......)))))))))))...))))..((((((.(..((((((......))))))..)..)))))) ( -66.60)
>DroYak_CAF1 910 118 + 1
CGGCUGGCAAAAAGCAGGCCGUACAAAGGAUUCAGCUUGGCCGCCUCGCCAAGAUCCAGCUGGGCGAGGCACAGGCCCUCCCUCAAGUGCUGCAGGCACCACUGCAAUGCCCUGAAGG
.(((((((...((((...((.......)).....)))).)))((((((((.((......)).))))))))...))))...(((..((.(((((((......)))))..)).))..))) ( -48.80)
>DroAna_CAF1 14703 118 + 1
CGGCUGGCGAAGAGCAGCCCGUAAAGUGGGUUUAGCUUGGCGGCCUGGGCCAGGUCCUUUUGGGCGAGACUCAGUCCUCCUCUCAGGUACUCCAGGCACCACUGGAGCGCUGCAUAGA
...(((((...((((((((((.....))))))..))))(((((((((((....((((....))))(((........)))..))))))).((((((......)))))))))))).))). ( -45.20)
>consensus
CGGCUGGCAAAAAGCAGGCCGUACAAAGGGUUCAGCUUGGCCGCCUCGCCAAGAUCAAGCUGGGCGAGGCGCAGGCCCUCCCUCAAGUGCUGCAGGCACCACUGCAGUGCCCUGAAGG
.((((.((.....)).))))......((((....(((((..(((((((((.((......)).))))))))))))))...))))...(((((((((......)))))))))........ (-42.46 = -43.63 +   1.17)

alignment

secondary structure

dotplot

Window 3

Location	19,696,641 – 19,696,759
Length	118
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	87.63
Mean single sequence MFE	-53.25
Consensus MFE	-45.15
Energy contribution	-45.05
Covariance contribution	-0.10
Combinations/Pair	1.29
Mean z-score	-1.97
Structure conservation index	0.85
SVM decision value	0.59
SVM RNA-class probability	0.793172
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19696641 118 - 22224390
CCUUCAGGGCAUUGCAGUGGUGCCUGCAGCACUUGAGGGAGGGCCUGCGUCUCGCCCAGCUUGAUCUUGGCGAGGCGGCCAAGCUGAACCCUUUGUACGGCCUGCUUUUUGCCAGCCG
((((((((((..(((((......))))))).))))))))..(((..((((((((((.((......)).))))))))((((..((..........))..))))........))..))). ( -49.70)
>DroSec_CAF1 3122 118 - 1
CCUUCAGGGCACUGCAGUGGUGCCUGCAGCACCUGAGGGAAGGCCUGCGCCUCGCCCAGCUUGAUCUUGGCGAGGCGGCCAAGCUGAACCCUUUGUAUGGCCUGCUUUUUGCCAGCCG
((((((((...((((((......))))))..))))))))..(((..((((((((((.((......)).))))))))(((((.((..........)).)))))........))..))). ( -59.40)
>DroSim_CAF1 2292 118 - 1
CCUUCAGGGCACUGCAGUGGUGCCUGCAGCACCUGAGGGAGGGCCUGCGCCUCGCCCAGCUUGAUCUUGGCGAGGCGGCCAAGCUGAACCCUUUGUAUGGCCUGCUUUUUGCCAGCCG
((((((((...((((((......))))))..))))))))..(((..((((((((((.((......)).))))))))(((((.((..........)).)))))........))..))). ( -59.20)
>DroEre_CAF1 3392 118 - 1
CCUUCAGGGCACUGCAGUGGUGCCUGCAGCACUUGAAGGAGGGCUUGUGCCUCGCCCAGCUGGAUCUGGGCGAGGCGGCCAAGCUGAACCCUUUGUACGGCCUGCUUUUUGCCAGCCG
((((((((...((((((......))))))..))))))))..((((((((((((((((((......))))))))))))..))))))............((((..((.....))..)))) ( -61.20)
>DroYak_CAF1 910 118 - 1
CCUUCAGGGCAUUGCAGUGGUGCCUGCAGCACUUGAGGGAGGGCCUGUGCCUCGCCCAGCUGGAUCUUGGCGAGGCGGCCAAGCUGAAUCCUUUGUACGGCCUGCUUUUUGCCAGCCG
((((((((((..(((((......))))))).))))))))..((((...((((((((.((......)).)))))))))))).................((((..((.....))..)))) ( -52.30)
>DroAna_CAF1 14703 118 - 1
UCUAUGCAGCGCUCCAGUGGUGCCUGGAGUACCUGAGAGGAGGACUGAGUCUCGCCCAAAAGGACCUGGCCCAGGCCGCCAAGCUAAACCCACUUUACGGGCUGCUCUUCGCCAGCCG
.....((((((((((((......)))))))..(((((((..((....((..(.((((....))....(((....))))).)..))...))..)))).))))))))............. ( -37.70)
>consensus
CCUUCAGGGCACUGCAGUGGUGCCUGCAGCACCUGAGGGAGGGCCUGCGCCUCGCCCAGCUGGAUCUUGGCGAGGCGGCCAAGCUGAACCCUUUGUACGGCCUGCUUUUUGCCAGCCG
((((((((...((((((......))))))..))))))))..((((...((((((((.((......)).)))))))))))).................((((..((.....))..)))) (-45.15 = -45.05 +  -0.10)

alignment

secondary structure

dotplot

Window 4

Location	19,696,681 – 19,696,784
Length	103
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	79.06
Mean single sequence MFE	-48.38
Consensus MFE	-31.58
Energy contribution	-32.20
Covariance contribution	0.62
Combinations/Pair	1.21
Mean z-score	-2.37
Structure conservation index	0.65
SVM decision value	1.40
SVM RNA-class probability	0.949801
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19696681 103 + 22224390
CCGCCUCGCCAAGAUCAAGCUGGGCGAGACGCAGGCCCUCCCUCAAGUGCUGCAGGCACCACUGCAAUGCCCUGAAGGUAAGCGGCUCGUGGAUUGUGCCACC----
.((.((((((.((......)).)))))).))..((((((.(((..((.(((((((......)))))..)).))..)))..)).)))).((((......)))).---- ( -37.30)
>DroSec_CAF1 3162 103 + 1
CCGCCUCGCCAAGAUCAAGCUGGGCGAGGCGCAGGCCUUCCCUCAGGUGCUGCAGGCACCACUGCAGUGCCCUGAAGGUGAGCGGCUCGUGGAUUGUGCCACC----
.(((((((((.((......)).)))))))))..((((((((((((((..((((((......))))))..).))).))).))).)))).((((......)))).---- ( -55.80)
>DroSim_CAF1 2332 103 + 1
CCGCCUCGCCAAGAUCAAGCUGGGCGAGGCGCAGGCCCUCCCUCAGGUGCUGCAGGCACCACUGCAGUGCCCUGAAGGUAAGCGGCUCGUAGGAUGGGCCACC----
.(((((((((.((......)).)))))))))..((((((((.(((((..((((((......))))))..).))))......(((...))).))).)))))...---- ( -55.80)
>DroEre_CAF1 3432 107 + 1
CCGCCUCGCCCAGAUCCAGCUGGGCGAGGCACAAGCCCUCCUUCAAGUGCUGCAGGCACCACUGCAGUGCCCUGAAGGUUAGCGGCGCGUGGAUUGUGUCCGGCGUG
..(((((((((((......)))))))))))....((...((((((.(..((((((......))))))..)..))))))...)).((((.(((((...))))))))). ( -61.20)
>DroYak_CAF1 950 103 + 1
CCGCCUCGCCAAGAUCCAGCUGGGCGAGGCACAGGCCCUCCCUCAAGUGCUGCAGGCACCACUGCAAUGCCCUGAAGGUAAGCGGCUCGUGGUUGGUAUCCCC----
((((((((((.((......)).))))))))((..(((((.(((..((.(((((((......)))))..)).))..)))..)).)))..))))...........---- ( -41.50)
>DroAna_CAF1 14743 107 + 1
CGGCCUGGGCCAGGUCCUUUUGGGCGAGACUCAGUCCUCCUCUCAGGUACUCCAGGCACCACUGGAGCGCUGCAUAGAUCCUGGGUUCCUCGCUUAUCCCCUGCGGA
(.((..((((((((....)))))(((((((((((...((......((..((((((......))))))..)).....))..))))))..))))).....))).)).). ( -38.70)
>consensus
CCGCCUCGCCAAGAUCAAGCUGGGCGAGGCGCAGGCCCUCCCUCAAGUGCUGCAGGCACCACUGCAGUGCCCUGAAGGUAAGCGGCUCGUGGAUUGUGCCACC____
((((((((((.((......)).))))))))((..(((...(((...(((((((((......))))))))).....))).....)))..))))............... (-31.58 = -32.20 +   0.62)

alignment

secondary structure

dotplot

Window 5

Location	19,696,681 – 19,696,784
Length	103
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	79.06
Mean single sequence MFE	-48.82
Consensus MFE	-36.97
Energy contribution	-37.20
Covariance contribution	0.23
Combinations/Pair	1.32
Mean z-score	-1.80
Structure conservation index	0.76
SVM decision value	1.08
SVM RNA-class probability	0.912325
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19696681 103 - 22224390
----GGUGGCACAAUCCACGAGCCGCUUACCUUCAGGGCAUUGCAGUGGUGCCUGCAGCACUUGAGGGAGGGCCUGCGUCUCGCCCAGCUUGAUCUUGGCGAGGCGG
----.((((......))))..((.(((..((((((((((..(((((......))))))).))))))))..)))..))((((((((.((......)).)))))))).. ( -46.50)
>DroSec_CAF1 3162 103 - 1
----GGUGGCACAAUCCACGAGCCGCUCACCUUCAGGGCACUGCAGUGGUGCCUGCAGCACCUGAGGGAAGGCCUGCGCCUCGCCCAGCUUGAUCUUGGCGAGGCGG
----.((((......))))..(((.....((((((((...((((((......))))))..))))))))..)))...(((((((((.((......)).))))))))). ( -51.90)
>DroSim_CAF1 2332 103 - 1
----GGUGGCCCAUCCUACGAGCCGCUUACCUUCAGGGCACUGCAGUGGUGCCUGCAGCACCUGAGGGAGGGCCUGCGCCUCGCCCAGCUUGAUCUUGGCGAGGCGG
----...(((((.((....))........((((((((...((((((......))))))..)))))))).)))))..(((((((((.((......)).))))))))). ( -54.10)
>DroEre_CAF1 3432 107 - 1
CACGCCGGACACAAUCCACGCGCCGCUAACCUUCAGGGCACUGCAGUGGUGCCUGCAGCACUUGAAGGAGGGCUUGUGCCUCGCCCAGCUGGAUCUGGGCGAGGCGG
..(((.(((.....)))..)))(((((..((((((((...((((((......))))))..))))))))..)))....(((((((((((......))))))))))))) ( -55.80)
>DroYak_CAF1 950 103 - 1
----GGGGAUACCAACCACGAGCCGCUUACCUUCAGGGCAUUGCAGUGGUGCCUGCAGCACUUGAGGGAGGGCCUGUGCCUCGCCCAGCUGGAUCUUGGCGAGGCGG
----.((....))..(((((.(((.((..((((((((((..(((((......))))))).))))))))))))).)))((((((((.((......)).)))))))))) ( -47.20)
>DroAna_CAF1 14743 107 - 1
UCCGCAGGGGAUAAGCGAGGAACCCAGGAUCUAUGCAGCGCUCCAGUGGUGCCUGGAGUACCUGAGAGGAGGACUGAGUCUCGCCCAAAAGGACCUGGCCCAGGCCG
(((....((.....((((((....(((..(((...(((.(((((((......)))))))..)))...)))...)))..))))))))....)))...(((....))). ( -37.40)
>consensus
____GGGGGCACAAUCCACGAGCCGCUUACCUUCAGGGCACUGCAGUGGUGCCUGCAGCACCUGAGGGAGGGCCUGCGCCUCGCCCAGCUGGAUCUUGGCGAGGCGG
........................(((..((((((((...((((((......))))))..))))))))..)))...(((((((((.((......)).))))))))). (-36.97 = -37.20 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:50:32 2006