Locus 1646

Sequence ID	3L_DroMel_CAF1
Location	4,768,736 – 4,768,975
Length	239
Max. P	0.973059

overview

Window 7

Location	4,768,736 – 4,768,826
Length	90
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	92.98
Mean single sequence MFE	-33.08
Consensus MFE	-31.02
Energy contribution	-31.10
Covariance contribution	0.08
Combinations/Pair	1.04
Mean z-score	-1.07
Structure conservation index	0.94
SVM decision value	0.01
SVM RNA-class probability	0.536894
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4768736 90 - 23771897
---------GCAUUGGGCUUGUAAAUGGGCUUUUAUUUUCGUUUGCCGGGUUAAGAGCCCGCACAAGGACGAAUGCCACCGCGACCA-AGACGCGGACGU
---------(((((.(.(((((...((((((((((..((((.....)))).)))))))))).)))))..).)))))..(((((....-...))))).... ( -34.70)
>DroSec_CAF1 31519 90 - 1
---------GCAGUGGGCUUGUAAAUGGGCUUUUAUUUUCGUUGGCCGGGUUAAGAGCCCGCACAAGGACGAAUGCCACCGCGGCCA-AGACGCGGACGC
---------(((.((..(((((...((((((((((..((((.....)))).)))))))))).)))))..))..)))..(((((....-...))))).... ( -32.90)
>DroSim_CAF1 30488 90 - 1
---------GCAGUGGGCUUGUAAAUGGGCUUUUAUUUUCGUUGGCCGGGUUAAGAGCCUGCACAAGGACGAAUGCCACCGCGGCCA-AGACGCGGACGU
---------(((.((..(((((...((((((((((..((((.....)))).)))))))))).)))))..))..)))..(((((....-...))))).... ( -30.00)
>DroEre_CAF1 20780 91 - 1
---------GCAGUGGGCUUGUAAAUGGGCUUUUAUUUUCGUUGGCCGGGUUAAGAGCCCGCACAAGGACGAAUGCCACCGCGGCCAAAGACGCGGACGU
---------(((.((..(((((...((((((((((..((((.....)))).)))))))))).)))))..))..)))..(((((........))))).... ( -33.20)
>DroYak_CAF1 27906 99 - 1
CUGGCAGUGGCAGUGGGCUUGUAAAUGGGCUUUUAUUUUCGUUAGCCGGGUUAAGAGCCGGCACAAGGACGAAUGCCACCGCGGCCA-AGACGCGGACGU
.......(((((..((((((......)))))).....((((((.(((((.(....).))))).....)))))))))))(((((....-...))))).... ( -34.60)
>consensus
_________GCAGUGGGCUUGUAAAUGGGCUUUUAUUUUCGUUGGCCGGGUUAAGAGCCCGCACAAGGACGAAUGCCACCGCGGCCA_AGACGCGGACGU
.........(((..(..(((((...((((((((((..((((.....)))).)))))))))).)))))..)...)))..(((((........))))).... (-31.02 = -31.10 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	4,768,826 – 4,768,935
Length	109
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	91.07
Mean single sequence MFE	-36.62
Consensus MFE	-29.78
Energy contribution	-30.12
Covariance contribution	0.34
Combinations/Pair	1.06
Mean z-score	-2.07
Structure conservation index	0.81
SVM decision value	0.15
SVM RNA-class probability	0.605483
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4768826 109 + 23771897
---CACAGUCAAGGACUUGAGCUUG------AGCCUGAGCCGGCUGGCAAUUCAAAUGCCAGGACACGAGGACA--UGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUC
---.((.((((.(..((((.((((.------.....))))...((((((.......))))))....))))..).--))))..(((((((.((((...)))).)))).)))...))..... ( -35.60)
>DroSec_CAF1 31609 109 + 1
---CACAGUCAAGGACUUGAGCUUG------AGCCUGAGCCGGCUGGCAAUUCAAAUGCCAGGACACAAGGACA--UGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUC
---.((.((((.(..((((.((((.------.....))))...((((((.......))))))....))))..).--))))..(((((((.((((...)))).)))).)))...))..... ( -35.90)
>DroSim_CAF1 30578 109 + 1
---CACAGUCAAGGACUUGAGCUUG------AGCCUGAGCCGGCUGGCAAUUCAAAUGCCAGGACACGAGGACA--UGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUC
---.((.((((.(..((((.((((.------.....))))...((((((.......))))))....))))..).--))))..(((((((.((((...)))).)))).)))...))..... ( -35.60)
>DroEre_CAF1 20871 115 + 1
---CACAGUCAAGGACUUCAGCUUGAGCCUGAGCCUGAGCCGGCUGGCAAUUCAAAUGCCAGGACACGAGGACU--UGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUC
---.((.((((((..((((.((((..((....))..))))...((((((.......)))))).....)))).))--))))..(((((((.((((...)))).)))).)))...))..... ( -39.90)
>DroYak_CAF1 28005 112 + 1
UGCCACAGUCAAGGACUUGAGCUUG------AGCCUGAGCCGGCUGGCAAUUCAAAUGCCAGGACACAAGGACA--UGGCAGGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUC
(((((..(((..((.(((..((...------.))..)))))..((((((.......))))))........))).--))))).(((((((.((((...)))).)))).))).......... ( -38.20)
>DroAna_CAF1 21796 110 + 1
UGCCACAGUCAAGGACUUGAGCC---------G-CUUGGCAGCCUAGCAAUUCAAAUGCCAAGAGACGAGGACAGCCGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUC
(((.........(..((((....---------.-(((((((....(....).....)))))))...))))..).((((..(((((((....)))...))))..)))).)))......... ( -34.50)
>consensus
___CACAGUCAAGGACUUGAGCUUG______AGCCUGAGCCGGCUGGCAAUUCAAAUGCCAGGACACGAGGACA__UGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUC
....((.((((.(..((((.((((............))))...((((((.......))))))....))))..)...))))..(((((((.((((...)))).)))).)))...))..... (-29.78 = -30.12 +   0.34)

alignment

secondary structure

dotplot

Window 9

Location	4,768,857 – 4,768,975
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	96.46
Mean single sequence MFE	-29.72
Consensus MFE	-26.29
Energy contribution	-26.48
Covariance contribution	0.19
Combinations/Pair	1.04
Mean z-score	-2.01
Structure conservation index	0.88
SVM decision value	1.70
SVM RNA-class probability	0.973059
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4768857 118 + 23771897
CGGCUGGCAAUUCAAAUGCCAGGACACGAGGACA--UGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUCACCCAAUUUACCAUAAAUAAAGAUACGUACAUAUUGUCAG
...((((((((.....((((((..(....)..).--))))).(((((((.((((...)))).)))).)))...((((((......)))))).....................)))))))) ( -30.10)
>DroSec_CAF1 31640 118 + 1
CGGCUGGCAAUUCAAAUGCCAGGACACAAGGACA--UGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUCACCCAAUUUACCAUAAAUAAAGAUAUGUACAUAUUGUCAG
...((((((.......))))))((((....((((--((.(..(((((((.((((...)))).)))).)))...((((((......))))))..........).))))).)....)))).. ( -31.10)
>DroSim_CAF1 30609 118 + 1
CGGCUGGCAAUUCAAAUGCCAGGACACGAGGACA--UGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUCACCCAAUUUACCAUAAAUAAAGAUACGUACAUAUUGUCAG
...((((((((.....((((((..(....)..).--))))).(((((((.((((...)))).)))).)))...((((((......)))))).....................)))))))) ( -30.10)
>DroEre_CAF1 20908 118 + 1
CGGCUGGCAAUUCAAAUGCCAGGACACGAGGACU--UGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUCACCCAAUUUACCAUAAAUAAAGAUACGUACAUAUUGUCAG
...((((((((.....(((((((.(.....).))--))))).(((((((.((((...)))).)))).)))...((((((......)))))).....................)))))))) ( -31.00)
>DroYak_CAF1 28039 118 + 1
CGGCUGGCAAUUCAAAUGCCAGGACACAAGGACA--UGGCAGGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUCACCCAAUUUACCAUAAAUAAAGAUACGUACAUAUUGUCAG
...((((((((.....((((((..(....)..).--))))).(((((((.((((...)))).)))).)))...((((((......)))))).....................)))))))) ( -29.90)
>DroAna_CAF1 21826 120 + 1
AGCCUAGCAAUUCAAAUGCCAAGAGACGAGGACAGCCGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUCACCCAAUUUACCAUAAAUAAAGAUACGUACAUAUUGUCAG
......(((.......))).....(((((.(((.((((..(((((((....)))...))))..))))......((((((......))))))...............)).)...))))).. ( -26.10)
>consensus
CGGCUGGCAAUUCAAAUGCCAGGACACGAGGACA__UGGCAAGCGCUGAAAAGCAAAGCUUAUCGGCCGCAACGUAAAUCACCCAAUUUACCAUAAAUAAAGAUACGUACAUAUUGUCAG
...((((((.......))))))...............((((((((((((.((((...)))).)))).)))...((((((......))))))......................))))).. (-26.29 = -26.48 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:47 2006