Locus 2108

Sequence ID	2R_DroMel_CAF1
Location	7,897,369 – 7,897,524
Length	155
Max. P	0.988971

overview

Window 3

Location	7,897,369 – 7,897,465
Length	96
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	93.88
Mean single sequence MFE	-29.52
Consensus MFE	-25.06
Energy contribution	-25.38
Covariance contribution	0.32
Combinations/Pair	1.07
Mean z-score	-2.10
Structure conservation index	0.85
SVM decision value	2.14
SVM RNA-class probability	0.988971
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7897369 96 + 20766785
GUGACUAAAGUGAAUGAUGCUCCAUGAUUCAUGGGGUGAAGAAACCCUGGUCACUCACUUAAUUGAUUCCAGGCAAUCGAUGGAUCAUCGACGGGG-
((((((...((((((.(((...))).))))))(((((......)))))))))))...(((..(((((((((.........))))..)))))..)))- ( -28.10)
>DroSec_CAF1 1819 96 + 1
GUGACUCAAGUGAAUGAUGCUCCAUGAUUCAUGGGGUUAAGAAACCCUGGUCACUCACUUAAUCGAUUCCAGACAAUCGAUGGAUCAUCGAAGUGG-
((((((...((((((.(((...))).))))))((((((....)))))))))))).((((...(((((((((.........))))..))))))))).- ( -31.40)
>DroSim_CAF1 1817 96 + 1
GUGACUCAAGUGAAUGAUGCUCCAUGAUUCAUGGGGUUAAGAAACCCUGGUCACUCACUUAAUCGAUUCCAGACAAUCGAUGGAUCAUCGAAGUGG-
((((((...((((((.(((...))).))))))((((((....)))))))))))).((((...(((((((((.........))))..))))))))).- ( -31.40)
>DroEre_CAF1 1810 97 + 1
GUGACUAAAGUGAAUGAUGCUCCAUGAUUCAUGGGGUUAAGAAACCCCGGGCCCUCAAUUAAUUGAUUCCAGACAAUCGAUGGAUCAUCGACGGGGU
.(((((...((((((.(((...))).))))))..)))))....((((((((...((((....))))..))......((((((...)))))))))))) ( -30.00)
>DroYak_CAF1 1828 96 + 1
GUGACUAAAGUGAAUGAUGCUCCAUGAUUCAUGGGGUUAAGAAACCCCGGCCACUCAAUUAAUUGAUUCCAGACAAUCGAUGGAUCAUCGACGGGG-
.(((((...((((((.(((...))).))))))..))))).....(((((.....((((....))))..........((((((...)))))))))))- ( -26.70)
>consensus
GUGACUAAAGUGAAUGAUGCUCCAUGAUUCAUGGGGUUAAGAAACCCUGGUCACUCACUUAAUUGAUUCCAGACAAUCGAUGGAUCAUCGACGGGG_
((((((...((((((.(((...))).))))))((((((....))))))))))))........(((((((((.........))))..)))))...... (-25.06 = -25.38 +   0.32)

alignment

secondary structure

dotplot

Window 4

Location	7,897,369 – 7,897,465
Length	96
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	93.88
Mean single sequence MFE	-27.78
Consensus MFE	-22.12
Energy contribution	-21.84
Covariance contribution	-0.28
Combinations/Pair	1.08
Mean z-score	-2.35
Structure conservation index	0.80
SVM decision value	1.58
SVM RNA-class probability	0.965117
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7897369 96 - 20766785
-CCCCGUCGAUGAUCCAUCGAUUGCCUGGAAUCAAUUAAGUGAGUGACCAGGGUUUCUUCACCCCAUGAAUCAUGGAGCAUCAUUCACUUUAGUCAC
-..(((((((((...))))))).....))........((((((((((...((((......))))((((...)))).....))))))))))....... ( -23.70)
>DroSec_CAF1 1819 96 - 1
-CCACUUCGAUGAUCCAUCGAUUGUCUGGAAUCGAUUAAGUGAGUGACCAGGGUUUCUUAACCCCAUGAAUCAUGGAGCAUCAUUCACUUGAGUCAC
-(((..((((((...)))))).....)))....((((((((((((((...(((((....)))))((((...)))).....)))))))))))).)).. ( -29.80)
>DroSim_CAF1 1817 96 - 1
-CCACUUCGAUGAUCCAUCGAUUGUCUGGAAUCGAUUAAGUGAGUGACCAGGGUUUCUUAACCCCAUGAAUCAUGGAGCAUCAUUCACUUGAGUCAC
-(((..((((((...)))))).....)))....((((((((((((((...(((((....)))))((((...)))).....)))))))))))).)).. ( -29.80)
>DroEre_CAF1 1810 97 - 1
ACCCCGUCGAUGAUCCAUCGAUUGUCUGGAAUCAAUUAAUUGAGGGCCCGGGGUUUCUUAACCCCAUGAAUCAUGGAGCAUCAUUCACUUUAGUCAC
........((((.(((((.((((....((..((((....))))...)).((((((....))))))...))))))))).))))............... ( -27.70)
>DroYak_CAF1 1828 96 - 1
-CCCCGUCGAUGAUCCAUCGAUUGUCUGGAAUCAAUUAAUUGAGUGGCCGGGGUUUCUUAACCCCAUGAAUCAUGGAGCAUCAUUCACUUUAGUCAC
-.......((((.(((((.((((....((..((((....))))....))((((((....))))))...))))))))).))))............... ( -27.90)
>consensus
_CCCCGUCGAUGAUCCAUCGAUUGUCUGGAAUCAAUUAAGUGAGUGACCAGGGUUUCUUAACCCCAUGAAUCAUGGAGCAUCAUUCACUUUAGUCAC
........((((.(((((.((((...(((..(((......)))....)))(((((....)))))....))))))))).))))............... (-22.12 = -21.84 +  -0.28)

alignment

secondary structure

dotplot

Window 5

Location	7,897,428 – 7,897,524
Length	96
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	81.81
Mean single sequence MFE	-26.98
Consensus MFE	-15.52
Energy contribution	-16.93
Covariance contribution	1.42
Combinations/Pair	1.17
Mean z-score	-3.52
Structure conservation index	0.57
SVM decision value	1.25
SVM RNA-class probability	0.936537
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7897428 96 + 20766785
U--AAUUGAUUCCAGGCAAUCGAUGGAUCAUCGACGGGG--AAUUAAAAAUUCUAUUAAAAUUGCAACUUGUUGAUAAGCCAACAGGUUAGCAAUGCCCC-
.--..((((((((......((((((...))))))...))--)))))).............((((((((((((((......))))))))).))))).....- ( -28.20)
>DroPse_CAF1 1859 87 + 1
UAUAAGUGAUUCCGUACGAUCGAUGGAUCGCUUGCAGGAAUGUGUAUGUAUUCUAUUAAAACUGCAA-------------CAACAGGUUAGCAUUUAUCU-
.(((((((...((...(((((....))))).(((((((((((......)))))........))))))-------------.....))....)))))))..- ( -18.50)
>DroSec_CAF1 1878 96 + 1
U--AAUCGAUUCCAGACAAUCGAUGGAUCAUCGAAGUGG--AAUUAAAAAUUCUAUUAAAAUUGCAACUUGUUGAUAAGCCAACAGGUUAGCAAUGCUCC-
.--..(((((((((.........))))..)))))(((((--(((.....))))))))...((((((((((((((......))))))))).))))).....- ( -27.80)
>DroSim_CAF1 1876 96 + 1
U--AAUCGAUUCCAGACAAUCGAUGGAUCAUCGAAGUGG--AAUUAAAAAUUCUAUUAAAAUUGCAACUUGUUGAUAAGCCAACAGGUUAGCAAUGCUCC-
.--..(((((((((.........))))..)))))(((((--(((.....))))))))...((((((((((((((......))))))))).))))).....- ( -27.80)
>DroEre_CAF1 1869 98 + 1
U--AAUUGAUUCCAGACAAUCGAUGGAUCAUCGACGGGGUCGAUUAAGAAUUCUAUUAAAACUGCAACUUGUUGAUAAGUCAACAGGUUAGCAAUUCUCC-
(--((((((((((......((((((...)))))).)))))))))))................(((((((((((((....)))))))))).))).......- ( -29.40)
>DroYak_CAF1 1887 97 + 1
U--AAUUGAUUCCAGACAAUCGAUGGAUCAUCGACGGGG--AAUUAAGAAUUCUAUUAAAAUUGCAACUUGUUGAUAAGCCAACAGGUUAGCAAUUUUCAC
.--..((((((((......((((((...))))))...))--))))))..........(((((((((((((((((......))))))))).))))))))... ( -30.20)
>consensus
U__AAUUGAUUCCAGACAAUCGAUGGAUCAUCGACGGGG__AAUUAAAAAUUCUAUUAAAAUUGCAACUUGUUGAUAAGCCAACAGGUUAGCAAUGCUCC_
.....(((((((((.........))))..)))))..........................((((((((((((((......))))))))).)))))...... (-15.52 = -16.93 +   1.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:30 2006