Locus 985

Sequence ID	3R_DroMel_CAF1
Location	3,165,802 – 3,166,068
Length	266
Max. P	0.970520

overview

Window 1

Location	3,165,802 – 3,165,922
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.25
Mean single sequence MFE	-30.71
Consensus MFE	-29.11
Energy contribution	-29.35
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.52
Structure conservation index	0.95
SVM decision value	1.66
SVM RNA-class probability	0.970520
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3165802 120 - 27905053
CACAUAAGUGGUAGUCCUGUCAAAGUCAAAAAUAAACGCAGCGACAAUAAUGAUUUAUGUGCGCCGAGUCGAAGAGAAAAGAUCCUGAUUCUGUGAAAGGAAGCCAAGGACUCGAGCAUU
(((((((((.((.(((((((.................)))).)))....)).))))))))).((((((((.....)).....((((..((((......))))....)))))))).))... ( -28.23)
>DroSec_CAF1 13884 120 - 1
CACAUAAGUGGUAGUCCUGUCAAAGUCAAAAAUAAACGCAGCGACAAUAAUGAUUUAUGUGCGCCGAGUCGAAGAGGAAAGAUCCUGAUUCUGUGAAAGGAAGCCAAGGACUCGAGCAUU
(((((((((.((.(((((((.................)))).)))....)).))))))))).((((((((....((((....))))..((((......))))......)))))).))... ( -31.73)
>DroSim_CAF1 16602 120 - 1
CACAUAAGUGGUAGUCCUGUCAAAGUCAAAAAUAAACGCAGCGACAAUAAUGAUUUAUGUGCGCCGAGUCGAAGAGGAAAGAUCCUGAUUCUGUAAAAGGAAGCCAAGGACUCGAGCAGU
(((((((((.((.(((((((.................)))).)))....)).))))))))).((((((((....((((....))))..((((......))))......)))))).))... ( -31.73)
>DroEre_CAF1 5557 120 - 1
CACAUAAGUGGUAGUCCUGUCAAAGUCAAAAAUAAACGCAGCGACAAUAAUGAUUUAUGGGCGCCGAGUCGAAAAGGAAAGCUCCUGAUUCUGCGAAAGGAAGCCCAGGACUCGAGCAUU
..(((((((.((.(((((((.................)))).)))....)).)))))))...(((((((((((.((((....))))..)))..(....).........)))))).))... ( -30.43)
>DroYak_CAF1 15133 120 - 1
CAUAUAAGUGGUAGUCCUGUCAAAGUCAAAAAUAAACGCAGCGACAAUAAUGAUUUAUGUGCGCCGAGUCGAAAAGGAAAGGUCCUGAUUCUGUGGAAGGAAGCCAAGGACUCGAGCAUU
(((((((((.((.(((((((.................)))).)))....)).))))))))).(((((((((((.((((....))))..)))..(((.......)))..)))))).))... ( -31.43)
>consensus
CACAUAAGUGGUAGUCCUGUCAAAGUCAAAAAUAAACGCAGCGACAAUAAUGAUUUAUGUGCGCCGAGUCGAAGAGGAAAGAUCCUGAUUCUGUGAAAGGAAGCCAAGGACUCGAGCAUU
(((((((((.((.(((((((.................)))).)))....)).))))))))).((((((((....((((....))))..((((......))))......)))))).))... (-29.11 = -29.35 +   0.24)

alignment

secondary structure

dotplot

Window 2

Location	3,165,842 – 3,165,962
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.36
Mean single sequence MFE	-30.90
Consensus MFE	-27.94
Energy contribution	-27.62
Covariance contribution	-0.32
Combinations/Pair	1.12
Mean z-score	-1.39
Structure conservation index	0.90
SVM decision value	0.93
SVM RNA-class probability	0.883108
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3165842 120 + 27905053
UUUUCUCUUCGACUCGGCGCACAUAAAUCAUUAUUGUCGCUGCGUUUAUUUUUGACUUUGACAGGACUACCACUUAUGUGUUUAUGUCGGCGUUGAGAAGAAGAAGCUGAGAAGGACGAA
((((((((((..(((((((((((((((((((...(((((..(((........)).)..)))))((....))....))).))))))))..))))))))..)))))....)))))....... ( -31.70)
>DroSec_CAF1 13924 112 + 1
UUUCCUCUUCGACUCGGCGCACAUAAAUCAUUAUUGUCGCUGCGUUUAUUUUUGACUUUGACAGGACUACCACUUAUGUGUUUAUGUCGGCGUUGAGAAGGAGAAUCUGAGC--------
((((((..((((((((((((((((((........(((((..(((........)).)..)))))((....))..))))))))....))))).)))))..))))))........-------- ( -31.40)
>DroSim_CAF1 16642 112 + 1
UUUCCUCUUCGACUCGGCGCACAUAAAUCAUUAUUGUCGCUGCGUUUAUUUUUGACUUUGACAGGACUACCACUUAUGUGUUUAUGUCGGCGUUGAGAAGGAGAAUCUGAGC--------
((((((..((((((((((((((((((........(((((..(((........)).)..)))))((....))..))))))))....))))).)))))..))))))........-------- ( -31.40)
>DroEre_CAF1 5597 112 + 1
UUUCCUUUUCGACUCGGCGCCCAUAAAUCAUUAUUGUCGCUGCGUUUAUUUUUGACUUUGACAGGACUACCACUUAUGUGUUUAUGUUGGCGUUGAGCAGGAGAAACCGAGC--------
.....(((((..(((((((((((((((((((...(((((..(((........)).)..)))))((....))....))).)))))))..)))))))))..)))))........-------- ( -29.40)
>DroYak_CAF1 15173 112 + 1
UUUCCUUUUCGACUCGGCGCACAUAAAUCAUUAUUGUCGCUGCGUUUAUUUUUGACUUUGACAGGACUACCACUUAUAUGGUUAUGUUGGCGUUGAGAAGGAGGAACUGAGC--------
(((((((((((((.(((((.(((...........)))))))).))).......(((.(..(((.....((((......))))..)))..).)))))))))))))........-------- ( -30.60)
>consensus
UUUCCUCUUCGACUCGGCGCACAUAAAUCAUUAUUGUCGCUGCGUUUAUUUUUGACUUUGACAGGACUACCACUUAUGUGUUUAUGUCGGCGUUGAGAAGGAGAAACUGAGC________
.....(((((..(((((((((((((((.(((...(((((..(((........)).)..)))))((....))......))))))))))..))))))))..)))))................ (-27.94 = -27.62 +  -0.32)

alignment

secondary structure

dotplot

Window 3

Location	3,165,962 – 3,166,068
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.69
Mean single sequence MFE	-28.04
Consensus MFE	-15.28
Energy contribution	-16.56
Covariance contribution	1.28
Combinations/Pair	1.12
Mean z-score	-2.14
Structure conservation index	0.54
SVM decision value	0.72
SVM RNA-class probability	0.831101
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3165962 106 + 27905053
GAAGGAAAAUGGAAUGUGACUCCCAAGGAGAAUGAAGAACAGUGGUAGACGUCUACCAAUUCAUUCUCAUUC---------AUAUUU-CUA-CUUCUUUAAACAUUUCAA---UAGAGAA
.((((((...(((((((((((....))(((((((((......((((((....)))))).)))))))))..))---------))))))-)..-.)))))).....((((..---..)))). ( -31.70)
>DroSec_CAF1 14036 114 + 1
--AGGAAAAUGGGAUGGGACUCCCAAGAAGAAUGAAGAAUAGUGGUAGACGUCUACCAAUUCAUUCUUAUUCUCAGCAGUAAUAUUUGUUA-CUUCUUUAAACAUUUCAU---UAGAGAA
--.......(((((((((...))))..(((((((((......((((((....)))))).)))))))))..)))))..((((((....))))-))(((((((........)---)))))). ( -31.50)
>DroSim_CAF1 16754 114 + 1
--AGGAAAAUGGGAUGGGACUCCCAAGGAGAAUGAAGAAUAGUGGUAGACGUCUACCAAUUCAUUCAUAUUCUCAGCAGUAAUAUUUGUUA-CUUCUUUAAACAUUUCAA---UAGAGAA
--..((((.(((((......)))))..(((((((((((((..((((((....)))))))))).)))))..))))((.((((((....))))-)).)).......))))..---....... ( -29.50)
>DroEre_CAF1 5709 118 + 1
--AGGAAAAUGGGAUGGGACUCACAAACAGCAUGGGGAAUAGUAGUAGACGUCUACCAAAUGAUUCUCAUUCGCAGCAGUAAUAUUUUUCAAGUUUUUCAAGGGAUUGCGAUCCCUUUAA
--.((((((((((((((((.(((((.......))..........((((....))))....))).))))))))((....))..)))))))).........(((((((....)))))))... ( -25.90)
>DroYak_CAF1 15285 115 + 1
--AGGAAAAUGGUAUGGGACUCCCAAGGAGCAUGAAGAAUAGUGGCAGACGUCUACCAAGUGAUUCUCAUUCGCAGCAGUACAAUUUGUUAACUUCUUGAAACAUUUGAA---CAGAAAA
--.(..(((((....((....))(((((((.((((.((((..(((.((....)).)))....))))))))....(((((......)))))..)))))))...)))))...---)...... ( -21.60)
>consensus
__AGGAAAAUGGGAUGGGACUCCCAAGGAGAAUGAAGAAUAGUGGUAGACGUCUACCAAUUCAUUCUCAUUCGCAGCAGUAAUAUUUGUUA_CUUCUUUAAACAUUUCAA___UAGAGAA
..(((((..(((((......)))))....((((((.((((..((((((....))))))....)))))))))).....................)))))...................... (-15.28 = -16.56 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:35 2006