Locus 2587

Sequence ID	3L_DroMel_CAF1
Location	7,199,378 – 7,199,531
Length	153
Max. P	0.999785

overview

Window 1

Location	7,199,378 – 7,199,497
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.82
Mean single sequence MFE	-35.24
Consensus MFE	-31.68
Energy contribution	-32.08
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-3.36
Structure conservation index	0.90
SVM decision value	4.07
SVM RNA-class probability	0.999785
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7199378 119 + 23771897
-UCUCUGGCUGCAGUGCAAUGCUUCUUCAUUCCUGGCAUUCGCACGUCACUCAGCAUCAAGCGGAAACAGUUAGCAACCAUCAUGGCUACCUCGCCAUCUUGCUUUCUCUCUCUCCCGCU
-......((((..((((((((((...........)))))).))))......))))....(((((....((..(((((.....(((((......))))).)))))..)).......))))) ( -32.90)
>DroSec_CAF1 12918 119 + 1
-UCUCUGGCUGCAGUGCAAUGCUUCUUCAUUCCUGGCAUUCGCACGUCACUCAGCAUCAAGCGGAAACAGUUAGCAACCAUCAUGGCUACCUCGCCAUCUUGCUCGCUCUCUCUCCCGCU
-......((((..((((((((((...........)))))).))))......))))....(((((....((..(((...((..(((((......)))))..))...)))..))...))))) ( -34.60)
>DroSim_CAF1 4872 119 + 1
-UCUCUGGCUGCAGUGCAAUGCUUCUUCAUUCCUGGCAUUCGCACGUCACUCAGCAUCAAGCGGAAACAGUUAGCAACCAUCAUGGCUACCUCGCCAUCUUGCUUGCUCUCUCUCCCGCU
-......((((..((((((((((...........)))))).))))......))))....(((((....((..(((((.((..(((((......)))))..)).)))))..))...))))) ( -38.50)
>DroEre_CAF1 13263 120 + 1
CUGGCUGGCUGCAGUGCAAUGCUUCUUCAUUCCUGGCAUUCGCACGUCACUCAGCAUCAAGCGGAAACAGUUAGCAACCAUCAUGGCUACCUCGCCAUCUUGCUUUCCCUCUCUCCCGCU
...((((..((..((((((((((...........)))))).))))..))..))))....(((((....((..(((((.....(((((......))))).)))))....)).....))))) ( -35.40)
>DroYak_CAF1 10392 119 + 1
-UGGCUGGCUGCAGUGCAAUGCUUCUUCAUUCCUGGCAUUCGCACGUCACUCAGCAUCAAGCGGAAACAGUUAGCAACCAUCAUGGCUACCUCGCCAUAUUGCUCUCCCUCUCUCCCGCU
-..((((..((..((((((((((...........)))))).))))..))..))))....(((((.....(..(((((.....(((((......))))).)))))..)........))))) ( -34.82)
>consensus
_UCUCUGGCUGCAGUGCAAUGCUUCUUCAUUCCUGGCAUUCGCACGUCACUCAGCAUCAAGCGGAAACAGUUAGCAACCAUCAUGGCUACCUCGCCAUCUUGCUUUCUCUCUCUCCCGCU
.......((((..((((((((((...........)))))).))))......))))....(((((....((..(((((.....(((((......))))).)))))..)).......))))) (-31.68 = -32.08 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	7,199,378 – 7,199,497
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.82
Mean single sequence MFE	-40.77
Consensus MFE	-37.22
Energy contribution	-36.74
Covariance contribution	-0.48
Combinations/Pair	1.06
Mean z-score	-2.23
Structure conservation index	0.91
SVM decision value	3.05
SVM RNA-class probability	0.998275
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7199378 119 - 23771897
AGCGGGAGAGAGAGAAAGCAAGAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCGAAUGCCAGGAAUGAAGAAGCAUUGCACUGCAGCCAGAGA-
((((((((((..((.((.((..(((((......)))))..)).)).))..)).))))))))....((((((((..((((...(..((....)).)...))))..)))).))))......- ( -36.60)
>DroSec_CAF1 12918 119 - 1
AGCGGGAGAGAGAGCGAGCAAGAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCGAAUGCCAGGAAUGAAGAAGCAUUGCACUGCAGCCAGAGA-
((((((((((..(((((.((..(((((......)))))..)).)))))..)).))))))))....((((((((..((((...(..((....)).)...))))..)))).))))......- ( -42.90)
>DroSim_CAF1 4872 119 - 1
AGCGGGAGAGAGAGCAAGCAAGAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCGAAUGCCAGGAAUGAAGAAGCAUUGCACUGCAGCCAGAGA-
((((((((((..(((((.((..(((((......)))))..)).)))))..)).))))))))....((((((((..((((...(..((....)).)...))))..)))).))))......- ( -43.20)
>DroEre_CAF1 13263 120 - 1
AGCGGGAGAGAGGGAAAGCAAGAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCGAAUGCCAGGAAUGAAGAAGCAUUGCACUGCAGCCAGCCAG
((((((((((..((.((.((..(((((......)))))..)).)).))..)).))))))))....((((..((..((((.(((((.............)))))))))..))..))))... ( -38.92)
>DroYak_CAF1 10392 119 - 1
AGCGGGAGAGAGGGAGAGCAAUAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCGAAUGCCAGGAAUGAAGAAGCAUUGCACUGCAGCCAGCCA-
((((((((...((...(((((((((((......)))))....))))))..)).))))))))....((((..((..((((.(((((.............)))))))))..))..))))..- ( -42.22)
>consensus
AGCGGGAGAGAGAGAAAGCAAGAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCGAAUGCCAGGAAUGAAGAAGCAUUGCACUGCAGCCAGAGA_
((((((((((..((.((.((..(((((......)))))..)).)).))..)).))))))))....((((((((..((((...(..((....)).)...))))..)))).))))....... (-37.22 = -36.74 +  -0.48)

alignment

secondary structure

dotplot

Window 3

Location	7,199,417 – 7,199,531
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.24
Mean single sequence MFE	-41.38
Consensus MFE	-29.71
Energy contribution	-29.75
Covariance contribution	0.04
Combinations/Pair	1.17
Mean z-score	-2.34
Structure conservation index	0.72
SVM decision value	0.90
SVM RNA-class probability	0.878287
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7199417 114 - 23771897
GGACACACACUCGCACGCUC-GCUGGCGGA-----AAGAGAGCGGGAGAGAGAGAAAGCAAGAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCG
...........((((((.((-(((((((..-----....(((((((((((..((.((.((..(((((......)))))..)).)).))..)).)))))))))..)))).))))))))))) ( -44.00)
>DroSec_CAF1 12957 109 - 1
GG-CACAUA----CACACUC-GCAGGCGGA-----AAGAGAGCGGGAGAGAGAGCGAGCAAGAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCG
.(-(((...----..(((((-(((((((((-----((.((..(....)....(((((.((..(((((......)))))..)).)))))..)).))))))))))....))))))..)))). ( -45.30)
>DroSim_CAF1 4911 110 - 1
GGACACAUA----CACACUC-GCAGGCGGA-----AAGAGAGCGGGAGAGAGAGCAAGCAAGAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCG
.........----..(((((-((.((((..-----....(((((((((((..(((((.((..(((((......)))))..)).)))))..)).)))))))))..))))..)))).))).. ( -42.00)
>DroEre_CAF1 13303 117 - 1
GGACACACACACACACGC---ACGCUUGCAGGCGGAAGAGAGCGGGAGAGAGGGAAAGCAAGAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCG
...............(((---(((.(..(.((((.....(((((((((((..((.((.((..(((((......)))))..)).)).))..)).)))))))))..))))..)..))))))) ( -41.50)
>DroYak_CAF1 10431 115 - 1
GGACGAACACACACACACUUAACACAUGAA-----AAGAGAGCGGGAGAGAGGGAGAGCAAUAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCG
...........(((.((((((.((..(...-----.)..(((((((((...((...(((((((((((......)))))....))))))..)).)))))))))..)).))))))..))).. ( -34.10)
>consensus
GGACACACAC_C_CACACUC_GCAGGCGGA_____AAGAGAGCGGGAGAGAGAGAAAGCAAGAUGGCGAGGUAGCCAUGAUGGUUGCUAACUGUUUCCGCUUGAUGCUGAGUGACGUGCG
...............(((((.(((...............(((((((((((..((.((.((..(((((......)))))..)).)).))..)).)))))))))..))).)))))....... (-29.71 = -29.75 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:36 2006