Locus 1965

Sequence ID	3R_DroMel_CAF1
Location	5,547,924 – 5,548,077
Length	153
Max. P	0.850260

overview

Window 3

Location	5,547,924 – 5,548,037
Length	113
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	83.15
Mean single sequence MFE	-41.66
Consensus MFE	-27.96
Energy contribution	-29.00
Covariance contribution	1.04
Combinations/Pair	1.14
Mean z-score	-1.82
Structure conservation index	0.67
SVM decision value	0.25
SVM RNA-class probability	0.651414
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5547924 113 - 27905053
UCCGGCAAUAAAUGCAGCAGCCGUUGCUGCUGCUGCUGC---CGCAACAAGUUCCACAUCUAACACAGCCUCCACAUCCAAGGAAGAGGGCAAGGAGGACGACUGGCAGCAGUGUC
...((((......((((((((....))))))))((((((---(.......(((........)))...((((((...(((........)))...))))).)....))))))).)))) ( -41.20)
>DroSec_CAF1 7007 113 - 1
UCCGGCAAUAAAUGCAGCAGCCGUUGCUGCUGCUGCCGC---CGCAACAAGUUCCACAUCCAACGCACCCUCCACAUCCAAGGAAGAGGGCAAGGAGGAUGACUGGCAGCAAUGUC
...((((......((((((((....))))))))(((.((---(((.....))....(((((..(...(((((....((....)).)))))...)..)))))...))).))).)))) ( -41.70)
>DroEre_CAF1 6213 116 - 1
UCCGGCAAUGAAUGCAGCAGCAGUUGCUGCUGCUGCUGCCGCCGCAACAAGUUCCUCAUCCAACGCAGCCUCCACAUCCAAGGAAGAGGGGAAGGAGGACGAUUGGCAGCAGUGUC
...((((......((((((((....))))))))((((((((.(((..(...((((((.(((....................))).))))))...)..).))..)))))))).)))) ( -43.65)
>DroYak_CAF1 6233 113 - 1
UCCAGCAAUGAAUGCAGCAGCCGUUGCCGCUGCUGCUGC---CGCAUCAAGUUCCUCAUCCAACACAGCCUCCACAUCCAAGGAAGAGGGAAAGGAGGACGACUGGCAGCAGUGUC
....((((((...((....))))))))(((((((((((.---(((.((...((((((.(((....................))).))))))...)).).)).).)))))))))).. ( -37.85)
>DroAna_CAF1 6932 116 - 1
CCCGGCAAUGAAUCAAGCAGCACCUGCAGCCGUGGCUUCCAACUCGGCUAGCACCAGCUCGAGUGCUGCUUCCACAUCGAAGGAGGAGGGCAAGGAAGAUGACUGGCAGCAGUGCC
...((((.((......((((...)))).(((((.((((((.((((((((......))).)))))(((.(((((........)))))..)))..))))).).)).)))..)).)))) ( -43.90)
>consensus
UCCGGCAAUGAAUGCAGCAGCCGUUGCUGCUGCUGCUGC___CGCAACAAGUUCCACAUCCAACGCAGCCUCCACAUCCAAGGAAGAGGGCAAGGAGGACGACUGGCAGCAGUGUC
...((((......((((((((....)))))))).(((((...........(((........)))....(((((...(((........)))...))))).......)))))..)))) (-27.96 = -29.00 +   1.04)

alignment

secondary structure

dotplot

Window 4

Location	5,547,964 – 5,548,077
Length	113
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	82.10
Mean single sequence MFE	-43.66
Consensus MFE	-28.84
Energy contribution	-30.24
Covariance contribution	1.40
Combinations/Pair	1.24
Mean z-score	-1.94
Structure conservation index	0.66
SVM decision value	0.50
SVM RNA-class probability	0.761547
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5547964 113 + 27905053
UGUGGAGGCUGUGUUAGAUGUGGAACUUGUUGCG---GCAGCAGCAGCAGCAACGGCUGCUGCAUUUAUUGCCGGAAAACGAACGGCAACAAAGUCGCCGUCGACCUUAAGCACCU
...((..(((..(((........)))..((((((---((.((.((((((((....)))))))).(((.((((((.........)))))).))))).)))).))))....))).)). ( -42.30)
>DroSec_CAF1 7047 113 + 1
UGUGGAGGGUGCGUUGGAUGUGGAACUUGUUGCG---GCGGCAGCAGCAGCAACGGCUGCUGCAUUUAUUGCCGGAAAUCGAACGGCCACAAAGUCUCCGUCGACCUUAAGAACCU
.((..(((((.((.(((((((((....((((.((---((((((((((((((....))))))))......)))))....))))))).))))).....)))).)))))))....)).. ( -41.40)
>DroEre_CAF1 6253 116 + 1
UGUGGAGGCUGCGUUGGAUGAGGAACUUGUUGCGGCGGCAGCAGCAGCAGCAACUGCUGCUGCAUUCAUUGCCGGAAAACGAACGGCAACAAAGUCGCCGUCGACCUUAAGCACCU
.....(((.((((((........)))..(((((((((((.((((((((((...)))))))))).....((((((.........))))))....))))))).)))).....)))))) ( -51.70)
>DroYak_CAF1 6273 113 + 1
UGUGGAGGCUGUGUUGGAUGAGGAACUUGAUGCG---GCAGCAGCAGCGGCAACGGCUGCUGCAUUCAUUGCUGGAAAACGAACGGCAACAAAGUCACCGUCGACCUUUAGCACCU
.(((((.(((((((..(.........)..)))))---)).(((((((((....).)))))))).)))))(((((((...(((.(((..((...))..))))))...)))))))... ( -41.60)
>DroAna_CAF1 6972 116 + 1
UGUGGAAGCAGCACUCGAGCUGGUGCUAGCCGAGUUGGAAGCCACGGCUGCAGGUGCUGCUUGAUUCAUUGCCGGGAAGCGAACGGCUACAAAGUCACCAUCUACUUUCAGCACUU
.(((((((((((((..((((((..(((..((.....)).)))..))))).)..))))))))(((((....((((.........)))).....)))))...)))))........... ( -41.30)
>consensus
UGUGGAGGCUGCGUUGGAUGUGGAACUUGUUGCG___GCAGCAGCAGCAGCAACGGCUGCUGCAUUCAUUGCCGGAAAACGAACGGCAACAAAGUCACCGUCGACCUUAAGCACCU
.....(((.(((....((((.(..(((((((((....))))).((((((((....)))))))).....((((((.........))))))..))))..)))))........)))))) (-28.84 = -30.24 +   1.40)

alignment

secondary structure

dotplot

Window 5

Location	5,547,964 – 5,548,077
Length	113
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	82.10
Mean single sequence MFE	-40.48
Consensus MFE	-26.90
Energy contribution	-28.62
Covariance contribution	1.72
Combinations/Pair	1.25
Mean z-score	-2.10
Structure conservation index	0.66
SVM decision value	0.79
SVM RNA-class probability	0.850260
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5547964 113 - 27905053
AGGUGCUUAAGGUCGACGGCGACUUUGUUGCCGUUCGUUUUCCGGCAAUAAAUGCAGCAGCCGUUGCUGCUGCUGCUGC---CGCAACAAGUUCCACAUCUAACACAGCCUCCACA
.((.((((..((.((((((((((...))))))).)))....))((((......((((((((....))))))))...)))---).....)))).))..................... ( -41.00)
>DroSec_CAF1 7047 113 - 1
AGGUUCUUAAGGUCGACGGAGACUUUGUGGCCGUUCGAUUUCCGGCAAUAAAUGCAGCAGCCGUUGCUGCUGCUGCCGC---CGCAACAAGUUCCACAUCCAACGCACCCUCCACA
..........(((((..((((((((((((((.....(.....)((((......((((((((....))))))))))))))---))))..))))).....)))..)).)))....... ( -37.10)
>DroEre_CAF1 6253 116 - 1
AGGUGCUUAAGGUCGACGGCGACUUUGUUGCCGUUCGUUUUCCGGCAAUGAAUGCAGCAGCAGUUGCUGCUGCUGCUGCCGCCGCAACAAGUUCCUCAUCCAACGCAGCCUCCACA
((((((.....((.(.(((((..((..((((((.........))))))..)).(((((((((((....))))))))))))))))).))..(((........)))))).)))..... ( -47.60)
>DroYak_CAF1 6273 113 - 1
AGGUGCUAAAGGUCGACGGUGACUUUGUUGCCGUUCGUUUUCCAGCAAUGAAUGCAGCAGCCGUUGCCGCUGCUGCUGC---CGCAUCAAGUUCCUCAUCCAACACAGCCUCCACA
.(((((....((.((((((..((...))..))).)))....))..........((((((((.((....)).))))))))---.)))))............................ ( -35.80)
>DroAna_CAF1 6972 116 - 1
AAGUGCUGAAAGUAGAUGGUGACUUUGUAGCCGUUCGCUUCCCGGCAAUGAAUCAAGCAGCACCUGCAGCCGUGGCUUCCAACUCGGCUAGCACCAGCUCGAGUGCUGCUUCCACA
...(((((.(((..((((((.((...)).))))))..)))..))))).......((((((((((((((((((.(........).))))).))).......).)))))))))..... ( -40.91)
>consensus
AGGUGCUUAAGGUCGACGGCGACUUUGUUGCCGUUCGUUUUCCGGCAAUGAAUGCAGCAGCCGUUGCUGCUGCUGCUGC___CGCAACAAGUUCCACAUCCAACGCAGCCUCCACA
.((.((((((((..(((((((((...)))))))))..)))).(((((......((((((((....)))))))))))))..........)))).))..................... (-26.90 = -28.62 +   1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:01 2006