Locus 2941

Sequence ID	2R_DroMel_CAF1
Location	10,167,602 – 10,167,827
Length	225
Max. P	0.970256

overview

Window 0

Location	10,167,602 – 10,167,707
Length	105
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.70
Mean single sequence MFE	-25.76
Consensus MFE	-18.56
Energy contribution	-19.04
Covariance contribution	0.48
Combinations/Pair	1.08
Mean z-score	-2.04
Structure conservation index	0.72
SVM decision value	0.94
SVM RNA-class probability	0.887117
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10167602 105 + 20766785
AUGGGAACAUACAUUUUCUUACGUUUAUUUUGAUGUGUGGCGGCAAAAGGGCGUGAAAUACGCCCAAAAAAAGGGAGACCGGAAGAGGAGGGUAAG---------------AAGCAGAGG
(((....)))....((((((((.(((.(((((.((.....)).)))))(((((((...))))))).......((....)).......))).)))))---------------)))...... ( -29.40)
>DroSec_CAF1 7388 87 + 1
AUGGGAAAAUACAUUUUCUUACGUUUAUUUUGAUGUGUGGCGGCAAAAGGGCGUGAAAUGCGCCCCAA-AAAGGGAGACCGGAAG--------------------------------AGG
.((((((((....))))))))......(((((.((.....)).)))))((((((.....))))))...-...((....)).....--------------------------------... ( -22.00)
>DroSim_CAF1 7319 104 + 1
AUGGGAAAAUACAUUUUCUUACGUUUAUUUUGAUGUGUGGCGGCAAAAGGGCGUGAAAUACGCCCCAA-AAAGGGAGACCGGAAGAGAGGGGUAAG---------------AAGCAGAGG
..............((((((((.(((.(((((.(((......)))...(((((((...))))))))))-)).((....)).......))).)))))---------------)))...... ( -26.40)
>DroEre_CAF1 7493 104 + 1
ACGGGAAAAUACAUUUUCUUACGUUUAUUAUGAUGUGUGGCGGCAAAAGGGCGUGAAAUACGCCCAAA-AAAGGCAGGCCGGAAAUGGAGGGAAAG---------------AAGCAGAGG
...........(((((((.((((((......)))))).(((.((....(((((((...)))))))...-....))..)))))))))).........---------------......... ( -26.90)
>DroYak_CAF1 7270 119 + 1
AUGGGGAAAUACAUUUUCUUUCGUUUAUUAUGAUGUGUGGCGGCAAAAGGGCAUGAAAUACGCCCAAA-AAAGGGAGACCGGAAAUGGAGGAAGAGCAGGGAGAGGAGGGAAAGCAGAGG
.............(((((((((.(((....((..(((((.((((......)).))...)))))(((..-...((....)).....)))........))...))).)))))))))...... ( -24.10)
>consensus
AUGGGAAAAUACAUUUUCUUACGUUUAUUUUGAUGUGUGGCGGCAAAAGGGCGUGAAAUACGCCCAAA_AAAGGGAGACCGGAAGAGGAGGGAAAG_______________AAGCAGAGG
..(((((((....))))))).(((((((......))).))))((....((((((.....)))))).......((....)).................................))..... (-18.56 = -19.04 +   0.48)

alignment

secondary structure

dotplot

Window 1

Location	10,167,682 – 10,167,787
Length	105
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	85.87
Mean single sequence MFE	-13.52
Consensus MFE	-11.60
Energy contribution	-11.35
Covariance contribution	-0.25
Combinations/Pair	1.22
Mean z-score	-1.54
Structure conservation index	0.86
SVM decision value	0.30
SVM RNA-class probability	0.677025
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10167682 105 - 20766785
CAAUUUGACAUAAAACCUUUGCCAGAUCCUUUUUUUGGCUCACGCAUGACACUUUAUGCAAAGUGCUUAUCCCUUCCCCGCCUCUGCUUCUUACCCUCCUCUUCC
................((((((((((.......))))))....((((((....))))))))))................((....)).................. ( -13.40)
>DroSec_CAF1 7467 88 - 1
CAAUUUGACAUAAAACCUUUGGCGGAUCCUUUUUUUGGCUCACGCAUGACACUUUAUGCAAAGUGCUCAUCCCUUCCCCACCU-----------------CUUCC
.....................(((((.((.......)).)).)))((((((((((....)))))).)))).............-----------------..... ( -14.50)
>DroSim_CAF1 7398 105 - 1
CAAUUUGACAUAAAACCUUUGCCGGAUCCUUUUUUUGGCUCACGCAUGACACUUUAUGCAAAGUGCUCAUCCCUUCCCCGCCUCUGCUUCUUACCCCUCUCUUCC
.....((((((.........((((((.......))))))....((((((....))))))...))).)))..........((....)).................. ( -14.50)
>DroEre_CAF1 7572 104 - 1
CAAUUUGACAUAAAACCUUUGCUGUAUCCUUU-UUCGGCUUACGCAUGACACUUUAUGCAAAGUGCUCAUCCCUUCCCCGCCUCUGCUUCUUUCCCUCCAUUUCC
((.((((.((((((.....(((.(((.((...-...))..))))))......)))))))))).))..............((....)).................. ( -11.70)
>consensus
CAAUUUGACAUAAAACCUUUGCCGGAUCCUUUUUUUGGCUCACGCAUGACACUUUAUGCAAAGUGCUCAUCCCUUCCCCGCCUCUGCUUCUUACCCUCCUCUUCC
.....((((((.........((((((.......))))))....((((((....))))))...))).))).................................... (-11.60 = -11.35 +  -0.25)

alignment

secondary structure

dotplot

Window 2

Location	10,167,707 – 10,167,827
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.58
Mean single sequence MFE	-29.34
Consensus MFE	-25.86
Energy contribution	-25.58
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-1.71
Structure conservation index	0.88
SVM decision value	1.66
SVM RNA-class probability	0.970256
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10167707 120 - 20766785
UUGGCAUUGAAAUCGAGCCGAGCUUUUCGGGCCUGUCUUUCAAUUUGACAUAAAACCUUUGCCAGAUCCUUUUUUUGGCUCACGCAUGACACUUUAUGCAAAGUGCUUAUCCCUUCCCCG
(((((.(((....))))))))......((((..((((.........))))......((((((((((.......))))))....((((((....)))))))))).............)))) ( -28.20)
>DroSec_CAF1 7475 120 - 1
UUGGCAUUGAAAUCGAGCCGAGCUUUUUGGGCCUGUCUUUCAAUUUGACAUAAAACCUUUGGCGGAUCCUUUUUUUGGCUCACGCAUGACACUUUAUGCAAAGUGCUCAUCCCUUCCCCA
..((((((......((((((((......((..(((((......(((......))).....)))))..))....))))))))..((((((....))))))..))))))............. ( -30.90)
>DroSim_CAF1 7423 120 - 1
UUGGCAUUGAAAUCGAGCCGAGCUUUUUGGGCCUGUCUUUCAAUUUGACAUAAAACCUUUGCCGGAUCCUUUUUUUGGCUCACGCAUGACACUUUAUGCAAAGUGCUCAUCCCUUCCCCG
..(((.(((....))))))((((.(((((((((((((.........)))).....((......))...........)))))..((((((....)))))))))).))))............ ( -30.50)
>DroEre_CAF1 7597 119 - 1
UUGGCAUUGAAAUUGAGCCGAGCUUUUUGGGCCUGUCUUUCAAUUUGACAUAAAACCUUUGCUGUAUCCUUU-UUCGGCUUACGCAUGACACUUUAUGCAAAGUGCUCAUCCCUUCCCCG
..((((((.....(((((((((((.....))).((((.........))))......................-.)))))))).((((((....))))))..))))))............. ( -26.80)
>DroYak_CAF1 7389 119 - 1
UUGGCAUUGAAAUUGAGCCAAGCUUUUUGGGCCUGUCUUUCAAUUUGACAUAAAACCUUUGUCGUAUCCUUU-UUUGGCCCACGCAUGACACUUUAUGCAAAGUGCUCAUCCCUUUCCCG
..((....((((.(((((...(((((.((((((............(((((.........)))))........-...)))))).((((((....))))))))))))))))....)))))). ( -30.30)
>consensus
UUGGCAUUGAAAUCGAGCCGAGCUUUUUGGGCCUGUCUUUCAAUUUGACAUAAAACCUUUGCCGGAUCCUUUUUUUGGCUCACGCAUGACACUUUAUGCAAAGUGCUCAUCCCUUCCCCG
..((((((......((((((((((.....))).((((.........))))........................)))))))..((((((....))))))..))))))............. (-25.86 = -25.58 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:21 2006