Locus 4536

Sequence ID	X_DroMel_CAF1
Location	11,952,622 – 11,952,775
Length	153
Max. P	0.988352

overview

Window 3

Location	11,952,622 – 11,952,735
Length	113
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	92.60
Mean single sequence MFE	-34.85
Consensus MFE	-30.62
Energy contribution	-31.50
Covariance contribution	0.88
Combinations/Pair	1.04
Mean z-score	-2.92
Structure conservation index	0.88
SVM decision value	2.12
SVM RNA-class probability	0.988352
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11952622 113 - 22224390
CAGGCCAAAUGGGGGAAUCCCGU---CUCCUUUGUGUGAUUCCCCUUUUUUUUGCCAGCAGCAGCAUUUGGCAU--GCGACCAUCACUAAAUCAGAAUCACAAACGCAUAUCACUCAA
...((((((((((((((((.((.---(......))).))))))))......((((.....))))))))))))((--(((.........................)))))......... ( -31.31)
>DroSim_CAF1 20069 114 - 1
CAGGCAAAAUGGGGGAAUCCCGCCGCCGCCUUUGUGUGAUUCCCCUUU--UUUGCCAGCUGCAGCGUUUGGCAU--GCGACCAUCACUAAAUCAGAAUCACAAACGCAUAUCACUCAA
..(((((((.(((((((((.(((..........))).))))))))).)--)))))).......(((((((....--.(................).....)))))))........... ( -36.89)
>DroEre_CAF1 20011 111 - 1
CAGGCGAAAUGGGGGAAUCCCGG---CUCUUUUGUGUGAUUCCCCUUU--UUUGCCAACUGCAGCGUUUGGCAU--GCGACCAUCACUAAAUCAGAAUCACAAACGCAUAUCAUUCAA
..(((((((.(((((((((.((.---(......))).))))))))).)--)))))).......(((((((....--.(................).....)))))))........... ( -35.09)
>DroYak_CAF1 19378 114 - 1
CAGGCAAAAUGGGGGAAUCCCGU---CUCUUUUGUGUGAUUCCCCUUU-UUUUGCCAGCUGCAGCGUUUGGCAUUGGCGACCAUCACUAAAUCAGAAUCACAAACGCAUAUCACUCAA
..(((((((.(((((((((.((.---(......))).)))))))))..-))))))).......(((((((((....))(.....)...............)))))))........... ( -36.10)
>consensus
CAGGCAAAAUGGGGGAAUCCCGU___CUCCUUUGUGUGAUUCCCCUUU__UUUGCCAGCUGCAGCGUUUGGCAU__GCGACCAUCACUAAAUCAGAAUCACAAACGCAUAUCACUCAA
..(((((((.(((((((((.((............)).)))))))))...))))))).......(((((((((....))(.....)...............)))))))........... (-30.62 = -31.50 +   0.88)

alignment

secondary structure

dotplot

Window 4

Location	11,952,662 – 11,952,775
Length	113
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	91.00
Mean single sequence MFE	-37.78
Consensus MFE	-30.13
Energy contribution	-31.32
Covariance contribution	1.19
Combinations/Pair	1.07
Mean z-score	-2.52
Structure conservation index	0.80
SVM decision value	1.25
SVM RNA-class probability	0.935552
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11952662 113 - 22224390
AAACAGAGAGUGAAAUCAGAGAAUCAAAACCAUUCUCGCACAGGCCAAAUGGGGGAAUCCCGU---CUCCUUUGUGUGAUUCCCCUUUUUUUUGCCAGCAGCAGCAUUUGGCAU--GC
.....(((((((..................)))))))(((...((((((((((((((((.((.---(......))).))))))))......((((.....)))))))))))).)--)) ( -37.27)
>DroSim_CAF1 20109 114 - 1
AAACAGAGAGUGAAAUCAGAGAACCAAAACCAUUCUCGCACAGGCAAAAUGGGGGAAUCCCGCCGCCGCCUUUGUGUGAUUCCCCUUU--UUUGCCAGCUGCAGCGUUUGGCAU--GC
((((.(((((((..................)))))))((((.(((((((.(((((((((.(((..........))).))))))))).)--)))))).).)))...)))).....--.. ( -39.97)
>DroEre_CAF1 20051 111 - 1
AAACAGAGAGUGAAAUCAGAGAACCAAAACCAUUCUCGCACAGGCGAAAUGGGGGAAUCCCGG---CUCUUUUGUGUGAUUCCCCUUU--UUUGCCAACUGCAGCGUUUGGCAU--GC
((((.(((((((..................)))))))(((..(((((((.(((((((((.((.---(......))).))))))))).)--))))))...)))...)))).....--.. ( -37.87)
>DroYak_CAF1 19418 114 - 1
AAACAGAGGCUGAAAUCAGAGAAACAAAACCAUUCCCGCACAGGCAAAAUGGGGGAAUCCCGU---CUCUUUUGUGUGAUUCCCCUUU-UUUUGCCAGCUGCAGCGUUUGGCAUUGGC
.........(((....))).....(((..(((..((.((((.(((((((.(((((((((.((.---(......))).)))))))))..-))))))).).))).).)..)))..))).. ( -36.00)
>consensus
AAACAGAGAGUGAAAUCAGAGAACCAAAACCAUUCUCGCACAGGCAAAAUGGGGGAAUCCCGU___CUCCUUUGUGUGAUUCCCCUUU__UUUGCCAGCUGCAGCGUUUGGCAU__GC
.....(((((((..................)))))))(((..(((((((.(((((((((.((............)).)))))))))...)))))))...))).((.....))...... (-30.13 = -31.32 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:37 2006