Locus 1510

Sequence ID	3R_DroMel_CAF1
Location	4,321,139 – 4,321,326
Length	187
Max. P	0.831383

overview

Window 3

Location	4,321,139 – 4,321,246
Length	107
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	89.14
Mean single sequence MFE	-39.23
Consensus MFE	-33.47
Energy contribution	-33.03
Covariance contribution	-0.44
Combinations/Pair	1.07
Mean z-score	-2.20
Structure conservation index	0.85
SVM decision value	0.64
SVM RNA-class probability	0.809335
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4321139 107 - 27905053
AGGGGCAAUAAAAGGCGCCAGUUAGCUAAGUGCUGGCUGCAUUGUGCCAAAGUGCGUUCACAGAUGAGUGGCCAACUGGUUAAGAGCACCGG-------------CAAAAGCAGAUUUUC
.((.((........)).))((((.(((...((((((.(((.((..((((...((.((.(((......)))))))..))))...)))))))))-------------))..))).))))... ( -32.50)
>DroSec_CAF1 8505 120 - 1
AGGGGCAAUAAAAGGCGCCAGUUAGCUAAGUGCUGGCUGCAUUGUGCCAAAGUGCGUUCACAGAUGAGUGGCCAACUGGUUAAGAGCACCGGCGGAAAGCCGAAGCAAAAGCAGAUUUUC
....((.......(((((((((((((.....))))))))....)))))....(((((((...(((.(((.....))).)))..))))..((((.....))))..)))...))........ ( -39.50)
>DroEre_CAF1 8508 119 - 1
AGGGGCAAUAAAAGGCGCCAGUUAGCUAAGUGCUGGCUGCAUUGUGCCAAAGUGCGUUCACAGAUGAGUGGCCAGCUGGCCAAGAGCACUGGCC-AAGGCAGAAGCAAAAGCAGAUUUUU
.((.((........)).))((((.(((...((((..((((.(((.((((..((((.((((....))))(((((....)))))...)))))))))-)).)))).))))..))).))))... ( -45.70)
>consensus
AGGGGCAAUAAAAGGCGCCAGUUAGCUAAGUGCUGGCUGCAUUGUGCCAAAGUGCGUUCACAGAUGAGUGGCCAACUGGUUAAGAGCACCGGC__AA_GC_GAAGCAAAAGCAGAUUUUC
....((.......(((((((((((((.....))))))))....)))))...((((.((((....))))(((((....)))))...)))).....................))........ (-33.47 = -33.03 +  -0.44)

alignment

secondary structure

dotplot

Window 4

Location	4,321,166 – 4,321,286
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.89
Mean single sequence MFE	-32.77
Consensus MFE	-31.30
Energy contribution	-31.64
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.96
SVM decision value	0.72
SVM RNA-class probability	0.831383
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4321166 120 + 27905053
ACCAGUUGGCCACUCAUCUGUGAACGCACUUUGGCACAAUGCAGCCAGCACUUAGCUAACUGGCGCCUUUUAUUGCCCCUUUUCCUCAUUCAUUGCUGGCCGGCAACAAAACGGUUUAAU
.((((((((((((......)))...((....((((........)))))).....))))))))).(((((((.(((((((..................))..))))).)))).)))..... ( -32.77)
>DroSec_CAF1 8545 120 + 1
ACCAGUUGGCCACUCAUCUGUGAACGCACUUUGGCACAAUGCAGCCAGCACUUAGCUAACUGGCGCCUUUUAUUGCCCCUUUUCCUCAUUCAUUGCUGGCCGGCAACAAAACGGUUUAAU
.((((((((((((......)))...((....((((........)))))).....))))))))).(((((((.(((((((..................))..))))).)))).)))..... ( -32.77)
>DroEre_CAF1 8547 120 + 1
GCCAGCUGGCCACUCAUCUGUGAACGCACUUUGGCACAAUGCAGCCAGCACUUAGCUAACUGGCGCCUUUUAUUGCCCCUUUUCCUCAUUCAUUGCUGGCCGGCAACAAAACGGUUUAAU
(((((.(((((((......)))...((....((((........)))))).....)))).)))))(((((((.(((((((..................))..))))).)))).)))..... ( -32.77)
>consensus
ACCAGUUGGCCACUCAUCUGUGAACGCACUUUGGCACAAUGCAGCCAGCACUUAGCUAACUGGCGCCUUUUAUUGCCCCUUUUCCUCAUUCAUUGCUGGCCGGCAACAAAACGGUUUAAU
.((((((((((((......)))...((....((((........)))))).....))))))))).(((((((.(((((((..................))..))))).)))).)))..... (-31.30 = -31.64 +   0.33)

alignment

secondary structure

dotplot

Window 5

Location	4,321,206 – 4,321,326
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-37.57
Consensus MFE	-37.72
Energy contribution	-37.50
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.45
Structure conservation index	1.00
SVM decision value	0.20
SVM RNA-class probability	0.629568
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4321206 120 - 27905053
GAACUGUUCCAGUGGCAGCUUCAUCGGAGCAGGAAACUAAAUUAAACCGUUUUGUUGCCGGCCAGCAAUGAAUGAGGAAAAGGGGCAAUAAAAGGCGCCAGUUAGCUAAGUGCUGGCUGC
...(((((((.((((.....)))).)))))))..............((..((..((((......))))..))...))....((.((........)).))(((((((.....))))))).. ( -37.00)
>DroSec_CAF1 8585 120 - 1
GAGCUGUUCCAGUGGCAGCUUCAUCGGAGCAGGAAACUAAAUUAAACCGUUUUGUUGCCGGCCAGCAAUGAAUGAGGAAAAGGGGCAAUAAAAGGCGCCAGUUAGCUAAGUGCUGGCUGC
...(((((((.((((.....)))).)))))))..............((..((..((((......))))..))...))....((.((........)).))(((((((.....))))))).. ( -36.70)
>DroEre_CAF1 8587 120 - 1
GAGCUGUUCCAGUGGCAGCUCCAUCGGAGCAGGAAACUAAAUUAAACCGUUUUGUUGCCGGCCAGCAAUGAAUGAGGAAAAGGGGCAAUAAAAGGCGCCAGUUAGCUAAGUGCUGGCUGC
..((((..((.(..((((((((...)))))((....))..............)))..).)).))))...............((.((........)).))(((((((.....))))))).. ( -39.00)
>consensus
GAGCUGUUCCAGUGGCAGCUUCAUCGGAGCAGGAAACUAAAUUAAACCGUUUUGUUGCCGGCCAGCAAUGAAUGAGGAAAAGGGGCAAUAAAAGGCGCCAGUUAGCUAAGUGCUGGCUGC
...(((((((.((((.....)))).)))))))..............((..((..((((......))))..))...))....((.((........)).))(((((((.....))))))).. (-37.72 = -37.50 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:30 2006