Locus 3300

Sequence ID	2R_DroMel_CAF1
Location	11,250,456 – 11,250,604
Length	148
Max. P	0.870300

overview

Window 3

Location	11,250,456 – 11,250,569
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.18
Mean single sequence MFE	-40.15
Consensus MFE	-26.33
Energy contribution	-25.97
Covariance contribution	-0.36
Combinations/Pair	1.14
Mean z-score	-1.74
Structure conservation index	0.66
SVM decision value	0.87
SVM RNA-class probability	0.870300
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11250456 113 + 20766785
ACUGUACGACGAUUCG------AGUAGCAGCAG-CGUGCUGCGGCCCAACAAAUGUUUGGCAGAACUCGAGCGUCUCUAUGCCGAAUUUCGCGCGAGUGAAAGCAGAUUCGAACGGGGUC
.((((..((((.((((------(((.(((((..-...))))).(((.(((....))).)))...))))))))))).......((((((((((....)))).....)))))).)))).... ( -44.20)
>DroVir_CAF1 4045 114 + 1
--CGUGU---AGCAGCAGUAGCAGCAGCAGCGA-CGUGCUGCGGCCCAACAAAUGUUUGGCAGAACUCGAACGCUUGUAUGCCGAAUUUCGCGCGAGUGAAAGUCUCUUCGAGCAUCGCC
--.....---.((((((((.((.......)).)-).))))))(((...((((.(((((((......))))))).))))((((((((((((((....)))))).....)))).)))).))) ( -38.20)
>DroPse_CAF1 40359 111 + 1
--CGUAU---AAAAACAGC---AGCGACGGCAG-CGUGCUGCGGCCCAACAAAUGUUUGGCAGAACUCGAGCGUCUGUACGCCGAAUUUCGCGCGAGUGAAAGUAGAUUUGAGCGGGGAA
--.....---.......((---(((.(((....-))))))))..(((.(((.((((((((......)))))))).))).(((((((((((((....)))).....)))))).)))))).. ( -38.10)
>DroGri_CAF1 4022 114 + 1
--CGUGU---CGCAGCAGCAACAGCAGCAGCGA-CGUGCUGCGGCCCAACAAAUGUUUGGCAGAACUCGAACGUUUGUAUGCCGAAUUUCGCGCGAGUGAAAGUCUCUUCGAGCAUCGCC
--...((---(((.((.((....)).)).))))-)(((.((((((...((((((((((((......))))))))))))..)))((.((((((....)))))).)).......))).))). ( -45.40)
>DroWil_CAF1 68031 103 + 1
-UCGUUU---GCGU----------CGUCGUCGGUGGUGCUGCGGCCCAACAAAUGUUUGGCAGAACUCGAACGUUUGUAUGCCGAAUUUCGCGCGAGUGAAAGUAGAUUUGAGCGUG---
-.(((((---(.((----------(....(((((((.((....)))).((((((((((((......))))))))))))..))))).((((((....))))))...))).))))))..--- ( -36.90)
>DroPer_CAF1 39872 111 + 1
--CGUAU---AAAAACAGC---AGCGACGGCAG-CGUGCUGCGGCCCAACAAAUGUUUGGCAGAACUCGAGCGUCUGUACGCCGAAUUUCGCGCGAGUGAAAGUAGAUUUGAGCGGGGAA
--.....---.......((---(((.(((....-))))))))..(((.(((.((((((((......)))))))).))).(((((((((((((....)))).....)))))).)))))).. ( -38.10)
>consensus
__CGUAU___AAAAACAGC___AGCAGCAGCAG_CGUGCUGCGGCCCAACAAAUGUUUGGCAGAACUCGAACGUCUGUAUGCCGAAUUUCGCGCGAGUGAAAGUAGAUUCGAGCGGGGAC
.......................((..(((((....)))))((((...(((.((((((((......)))))))).)))..))))..((((((....))))))..........))...... (-26.33 = -25.97 +  -0.36)

alignment

secondary structure

dotplot

Window 4

Location	11,250,489 – 11,250,604
Length	115
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.37
Mean single sequence MFE	-35.35
Consensus MFE	-21.67
Energy contribution	-21.75
Covariance contribution	0.08
Combinations/Pair	1.05
Mean z-score	-1.28
Structure conservation index	0.61
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11250489 115 + 20766785
GCGGCCCAACAAAUGUUUGGCAGAACUCGAGCGUCUCUAUGCCGAAUUUCGCGCGAGUGAAAGCAGAUUCGAACGGGGUCUGAUCCAGU-----GCCAGUUGGACAUUGAAAACGCCAAC
..(((......((((((..((.....(((.((((....))))))).((((((....)))))).(((((((.....))))))).......-----....))..))))))......)))... ( -36.70)
>DroVir_CAF1 4079 115 + 1
GCGGCCCAACAAAUGUUUGGCAGAACUCGAACGCUUGUAUGCCGAAUUUCGCGCGAGUGAAAGUCUCUUCGAGCAUCGCCUGAGCCAGG----CGCCAA-ACGAUAACGAUAUCGAUAAC
..............(((((((.((.((((((.((......)).((.((((((....)))))).))..))))))..))(((((...))))----))))))-))((((....))))...... ( -38.20)
>DroPse_CAF1 40390 112 + 1
GCGGCCCAACAAAUGUUUGGCAGAACUCGAGCGUCUGUACGCCGAAUUUCGCGCGAGUGAAAGUAGAUUUGAGCGGGGAACGGG---GC-----GCCAGUCGGAUAUUGAUAACGCCAAC
..(((......((((((((((.(....)(.((((((...(((((((((((((....)))).....)))))).)))(....).))---))-----))).))))))))))......)))... ( -36.60)
>DroGri_CAF1 4056 118 + 1
GCGGCCCAACAAAUGUUUGGCAGAACUCGAACGUUUGUAUGCCGAAUUUCGCGCGAGUGAAAGUCUCUUCGAGCAUCGCCUCAGUCAGAGUAACGAC-A-ACGAUACCGAUAACGAUAAC
.((((...((((((((((((......))))))))))))..))))..((((((....))))))(((...(((.(.((((.....(((........)))-.-.)))).))))....)))... ( -33.70)
>DroWil_CAF1 68057 92 + 1
GCGGCCCAACAAAUGUUUGGCAGAACUCGAACGUUUGUAUGCCGAAUUUCGCGCGAGUGAAAGUAGAUUUGAGCGUG-----AACUAGU-----G--A----------------GUCAAC
.((((...((((((((((((......))))))))))))..))))..((((((....))))))...((((((...(..-----..)...)-----)--)----------------)))... ( -29.70)
>DroPer_CAF1 39903 112 + 1
GCGGCCCAACAAAUGUUUGGCAGAACUCGAGCGUCUGUACGCCGAAUUUCGCGCGAGUGAAAGUAGAUUUGAGCGGGGAACGGG---AC-----GCCAGUCGGAUAUUGAUAACGCCAAC
..(((......((((((((((.(....)(.((((((...(((((((((((((....)))).....)))))).)))(....).))---))-----))).))))))))))......)))... ( -37.20)
>consensus
GCGGCCCAACAAAUGUUUGGCAGAACUCGAACGUCUGUAUGCCGAAUUUCGCGCGAGUGAAAGUAGAUUCGAGCGGGGACUGAGCCAGC_____GCCAG_AGGAUAUUGAUAACGCCAAC
.((((...(((.((((((((......)))))))).)))..))))..((((((....)))))).......................................................... (-21.67 = -21.75 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:11 2006