Locus 4221

Sequence ID	3R_DroMel_CAF1
Location	11,364,063 – 11,364,383
Length	320
Max. P	0.999649

overview

Window 2

Location	11,364,063 – 11,364,183
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.83
Mean single sequence MFE	-49.14
Consensus MFE	-45.68
Energy contribution	-45.88
Covariance contribution	0.20
Combinations/Pair	1.11
Mean z-score	-2.30
Structure conservation index	0.93
SVM decision value	3.83
SVM RNA-class probability	0.999649
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11364063 120 + 27905053
UAGUUGGGGAUAUCCCCCAACCGGUAAGAUUCCGUGGCGAUGAGAAACACGGACUGCAAAAAGGCCGCUUGGAGCACCUGCACCCAGGAGGCCCGAGGUCCGAGUCUUUCCUUCACCGGA
...((((((.....))))))((((((((((((.(((.(.....)...)))(((((.......((((.(((((.((....))..))))).))))...))))))))))))......))))). ( -48.60)
>DroSec_CAF1 111701 120 + 1
UAGUUGGGUAUAUCGCCCAACCGGUAAGAUUCCGUGGCGAUGAGAAAGACGGACUGCAAAAAGGCCGCUUGGAGCACCUGCACCCAGGUCGCCCGAGGUCCGAGUCUUUCCUUCACCGGA
..(((((((.....)))))))(((.......)))(((.((.(.(((((((((((.((......))..(((((.(((((((....))))).)))))))))))..)))))))).)).))).. ( -47.00)
>DroSim_CAF1 102735 120 + 1
UAGUUGGGUAUAUCGCCCAACCGGUAAGAUUCCGUGGCGAUGAGAAAGACGGACUGCAAAAAGGCCGCUUGGAGCACCUGCACCCAGGUGGCCCGAGGUCCAAGUCUUUCCUUCACCGGA
..(((((((.....)))))))(((.......)))(((.((.(.((((((((((((.......((((((((((.((....))..))))))))))...)))))..)))))))).)).))).. ( -52.00)
>DroEre_CAF1 99050 120 + 1
UAGUUGGGUAUAUCCCCCAACCGAUAAGAUUCCGUGGCGAUGAGGAAGACGGACUGCAAAAAGGCCGCUUGGAGCACCUGCACCCAGGUGGCCCGAGGUCCGAGCCUUUCCUUCACCGGA
..((((((.......)))))).........(((((((.(..((((....((((((.......((((((((((.((....))..))))))))))...))))))..))))..).))).)))) ( -48.10)
>DroYak_CAF1 101781 120 + 1
UAGUUGGGUAUAUCGCCCAACCGAUAGGAUUCCGUGGCGACGAGGAAGACGGACUGCAAGAAGGCCGCUUGGAGCACCUGCACCCAGGUGGCCCGAGGUCCGAGUCUCUCCUUCACCGGC
..(((((((.....))))))).((.((((((((.((....)).))))..((((((.......((((((((((.((....))..))))))))))...))))))......))))))...... ( -50.00)
>consensus
UAGUUGGGUAUAUCGCCCAACCGGUAAGAUUCCGUGGCGAUGAGAAAGACGGACUGCAAAAAGGCCGCUUGGAGCACCUGCACCCAGGUGGCCCGAGGUCCGAGUCUUUCCUUCACCGGA
..(((((((.....))))))).........(((((((.(..((((....((((((.......((((((((((.((....))..))))))))))...))))))..))))..).))).)))) (-45.68 = -45.88 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	11,364,063 – 11,364,183
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.83
Mean single sequence MFE	-47.88
Consensus MFE	-44.00
Energy contribution	-44.68
Covariance contribution	0.68
Combinations/Pair	1.05
Mean z-score	-1.75
Structure conservation index	0.92
SVM decision value	2.26
SVM RNA-class probability	0.991295
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11364063 120 - 27905053
UCCGGUGAAGGAAAGACUCGGACCUCGGGCCUCCUGGGUGCAGGUGCUCCAAGCGGCCUUUUUGCAGUCCGUGUUUCUCAUCGCCACGGAAUCUUACCGGUUGGGGGAUAUCCCCAACUA
...(((((..((.((((.(((((..((((((.(.((((.((....)))))).).)))))....)..))))).)))).)).))))).(((.......)))(((((((.....))))))).. ( -49.80)
>DroSec_CAF1 111701 120 - 1
UCCGGUGAAGGAAAGACUCGGACCUCGGGCGACCUGGGUGCAGGUGCUCCAAGCGGCCUUUUUGCAGUCCGUCUUUCUCAUCGCCACGGAAUCUUACCGGUUGGGCGAUAUACCCAACUA
...(((((.((((((((..((((...((((.(((((....))))))).))..((((.....)))).))))))))))))..))))).(((.......)))((((((.......)))))).. ( -47.20)
>DroSim_CAF1 102735 120 - 1
UCCGGUGAAGGAAAGACUUGGACCUCGGGCCACCUGGGUGCAGGUGCUCCAAGCGGCCUUUUUGCAGUCCGUCUUUCUCAUCGCCACGGAAUCUUACCGGUUGGGCGAUAUACCCAACUA
...(((((.((((((((..((((...((..((((((....))))))..))..((((.....)))).))))))))))))..))))).(((.......)))((((((.......)))))).. ( -48.60)
>DroEre_CAF1 99050 120 - 1
UCCGGUGAAGGAAAGGCUCGGACCUCGGGCCACCUGGGUGCAGGUGCUCCAAGCGGCCUUUUUGCAGUCCGUCUUCCUCAUCGCCACGGAAUCUUAUCGGUUGGGGGAUAUACCCAACUA
(((((((((((((.(((..((((...((..((((((....))))))..))..((((.....)))).))))))))))))..)))))..)))........(((((((.......))))))). ( -47.60)
>DroYak_CAF1 101781 120 - 1
GCCGGUGAAGGAGAGACUCGGACCUCGGGCCACCUGGGUGCAGGUGCUCCAAGCGGCCUUCUUGCAGUCCGUCUUCCUCGUCGCCACGGAAUCCUAUCGGUUGGGCGAUAUACCCAACUA
...(((((..(((..(..(((((...((..((((((....))))))..))..((((.....)))).)))))..)..))).))))).............(((((((.......))))))). ( -46.20)
>consensus
UCCGGUGAAGGAAAGACUCGGACCUCGGGCCACCUGGGUGCAGGUGCUCCAAGCGGCCUUUUUGCAGUCCGUCUUUCUCAUCGCCACGGAAUCUUACCGGUUGGGCGAUAUACCCAACUA
((((((((.((((((((..((((..((((((.(.((((.((....)))))).).)))))....)..))))))))))))..)))))..)))........(((((((.......))))))). (-44.00 = -44.68 +   0.68)

alignment

secondary structure

dotplot

Window 4

Location	11,364,183 – 11,364,303
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.33
Mean single sequence MFE	-43.38
Consensus MFE	-41.06
Energy contribution	-41.14
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-1.41
Structure conservation index	0.95
SVM decision value	1.24
SVM RNA-class probability	0.935062
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11364183 120 + 27905053
GCCAGUCGCUUGUUUAGAGUGUCGCAGGCUUUUCUCACUGCCAAUCCGAUCAUCUCGCUGGUCAUCGAGUUGGCCGUCAGCAUGGAGUUGGCUCCGUUUACAGUAUUGCUGGCCUCGACU
.......((((.....))))((((.((((.......((.(((((..((((.(((.....))).))))..))))).))(((((.((((....))))(....).....))))))))))))). ( -40.50)
>DroSec_CAF1 111821 120 + 1
GCCAGUCGCUUGUUCAGAGUGUCGCAGGCUUUUCUCACUGCCAAUCCGAUCAUCUCGCUGGUCAUCGAGUUGGCCGUCAGCAUGGAGUUGGCUCCGUUGACAGUAUUGCUAGCCUCCACU
....(.(((((.....))))).)(.(((((......((((((((..((((.(((.....))).))))..))))).((((((..((((....)))))))))))))......))))).)... ( -41.70)
>DroSim_CAF1 102855 120 + 1
GCCAGUCGCUUGUUCAGAGUGUCGCAGGCUUUUCUCACUGCCAAUCCGAUCAUCUCGCUGGUCAUCGAGUUGGCCGUCAGCAUGGAGUUGGCUCCGUUGACGGUAUUGCUAGCCUCCACU
....(.(((((.....))))).)(.(((((......((.(((((..((((.(((.....))).))))..)))))(((((((..((((....)))))))))))))......))))).)... ( -42.30)
>DroEre_CAF1 99170 120 + 1
GCCAGUCGCGUGUUCAGGGUGUCGCAGGCUUUUCUCACUGCCAGUCCGAUCAUCUCGCUGGUCAUCGAGUUGGCCGUCAGCAUGGAGUUGGCUCCGCUGACAGUAUUGCUGGCCUCCACU
((((((.(((............))).((((...(((..(((((((..(.....)..))))).))..)))..))))((((((..((((....))))))))))......))))))....... ( -45.00)
>DroYak_CAF1 101901 120 + 1
GCCAGUCGCUUGUUCAGAGUGUCGCAGGCUUUUCUCACUGCCAGUCCGAUCAUCUCGCUGGUCAUCGAGUUGGCCGUCAGCAUGGAGUUGGCUCCGCUGACGGUAUUGCUGGCCUCCACU
(((((((((((.....)))))..((((..........))))(((..((((.(((.....))).))))..)))(((((((((..((((....)))))))))))))...))))))....... ( -47.40)
>consensus
GCCAGUCGCUUGUUCAGAGUGUCGCAGGCUUUUCUCACUGCCAAUCCGAUCAUCUCGCUGGUCAUCGAGUUGGCCGUCAGCAUGGAGUUGGCUCCGUUGACAGUAUUGCUGGCCUCCACU
((((((.((((((..........)))))).......((((((((..((((.(((.....))).))))..))))).((((((..((((....)))))))))))))...))))))....... (-41.06 = -41.14 +   0.08)

alignment

secondary structure

dotplot

Window 5

Location	11,364,263 – 11,364,383
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.25
Mean single sequence MFE	-38.36
Consensus MFE	-33.12
Energy contribution	-32.72
Covariance contribution	-0.40
Combinations/Pair	1.15
Mean z-score	-1.44
Structure conservation index	0.86
SVM decision value	0.70
SVM RNA-class probability	0.827324
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11364263 120 + 27905053
CAUGGAGUUGGCUCCGUUUACAGUAUUGCUGGCCUCGACUCUCACCUGGUCCAACGGAACACCCAGCACGAAUGCUGCCACCUGGGCCGCCUUGGUGUUCACUCCUUGGCCAAUCUCAAU
..((..((((((((((((..(((.....))).....((((.......)))).))))))......(((((.((.((.(((.....))).)).)).))))).........))))))..)).. ( -36.50)
>DroSec_CAF1 111901 120 + 1
CAUGGAGUUGGCUCCGUUGACAGUAUUGCUAGCCUCCACUCUCACCUGGCCCAACGGAACACCCAACACGAAAGCUGCCACCUGGGCCGCCUUGGUGUUCACUCCUUGGCCAAUCUCAAU
..((..(((((((((((((..((.....)).(((.............))).)))))))......(((((.((.((.(((.....))).)).)).))))).........))))))..)).. ( -37.72)
>DroSim_CAF1 102935 120 + 1
CAUGGAGUUGGCUCCGUUGACGGUAUUGCUAGCCUCCACUCUCACCUGGUCCAACGGAACACCCAGCACGAAAGCUGCCACCUGGGCCGCCUUGGUGUUCACUCCUUGGCCAAUCUCAAU
..((((((((((.(((....)))....))))).)))))........(((.((((.(((......(((((.((.((.(((.....))).)).)).)))))...))))))))))........ ( -40.20)
>DroEre_CAF1 99250 120 + 1
CAUGGAGUUGGCUCCGCUGACAGUAUUGCUGGCCUCCACUCUCACCUGAUCCAACGGAACCCCCAGCACGAAUGCUGCCACCUGGGCCGCCUUGGUGUUCACUCCUUGGCCAAUCUCUAU
.((((((..(((((.(.((.((((((((((((..(((....((....))......)))....))))))...)))))).)).).)))))(((..((.(....).))..)))....)))))) ( -38.90)
>DroYak_CAF1 101981 120 + 1
CAUGGAGUUGGCUCCGCUGACGGUAUUGCUGGCCUCCACUUUCACCUGAUUUAGGGGAACGCCCAGCACGAAUGCUGCCACCUGGGCCGCCUUGGUGUUCACUCCCUGGCCAAUCUCAAU
....(((..(((((.(.((.(((((((((((((.(((.((.((....))...)).)))..).))))))...)))))).)).).)))))(((..((.(....).))..)))....)))... ( -38.50)
>consensus
CAUGGAGUUGGCUCCGUUGACAGUAUUGCUGGCCUCCACUCUCACCUGGUCCAACGGAACACCCAGCACGAAUGCUGCCACCUGGGCCGCCUUGGUGUUCACUCCUUGGCCAAUCUCAAU
....(((((((((((((((.(((...((..((......))..)).)))...)))))))......(((((.((.((.(((.....))).)).)).))))).........))))).)))... (-33.12 = -32.72 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:17 2006