Locus 1589

Sequence ID	3R_DroMel_CAF1
Location	4,561,263 – 4,561,374
Length	111
Max. P	0.814534

overview

Window 2

Location	4,561,263 – 4,561,374
Length	111
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	81.05
Mean single sequence MFE	-28.71
Consensus MFE	-17.45
Energy contribution	-18.37
Covariance contribution	0.92
Combinations/Pair	1.20
Mean z-score	-1.62
Structure conservation index	0.61
SVM decision value	-0.05
SVM RNA-class probability	0.509784
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4561263 111 + 27905053
AAGCAAAUAAAGGAUGCAUCACCCAUAAGGGCUCAAACUAUUGCCAAACUGCUACUGCGCGUGCGCAGCAGCUGACAAUCGAGCUUGUAAAUCCUAUGGUUAUUUAUUUGC
..(((((((((.(((.(((.........((((((.....((((.((....(((.(((((....))))).))))).)))).)))))).........)))))).))))))))) ( -28.87)
>DroSec_CAF1 18138 107 + 1
AAACAAAUAAAGGAUGCAUCUCCCACAAGGGCUCAGGCUAUUGCCAAACUGCUCCUGCGCAUGCGCAGCAGCUGAGAAUCGAGCUUGUAAAUCCUAUGGUUA----UUUGC
...(((((((((((((((.(((((....)).(((((((....))).....(((.(((((....))))).)))))))....)))..)))..)))))....)))----)))). ( -34.00)
>DroSim_CAF1 18838 107 + 1
AAACAAAUAAAGGAUGCAUCUCCCACAAGGGCUCAGGCUAUUGCCAAACUGCUCCUGCGCAUGCGCAGCAGCUGAGAAUCGAGCUUGUAAAUCCAAUGGUUA----UAUGC
...........(((((((.(((((....)).(((((((....))).....(((.(((((....))))).)))))))....)))..)))..))))........----..... ( -30.30)
>DroEre_CAF1 18579 107 + 1
AAACAAAUAAAGGAUGUAUCACCCACUAGGGCUCAGGCUAUUGCCAAACUGCUCCUGCGCAUGCGCAGCAGCUGAGAAUCGAGCUUGUAAAUCAUAUGGCUA----UUUGC
...((((((...(((......(((....)))(((((((....))).....(((.(((((....))))).))))))).)))..(((............)))))----)))). ( -29.60)
>DroYak_CAF1 18373 107 + 1
AAACAAAUAAAGGAUGUAUCAAUCACAAGAGCUCAGGCUAUUGCCAAAUUGCUACUGCGCAUGCGCAGCAGCUGAGAAUCGAGCUUGUAAAUCAUAUGGCUA----UUUGC
...((((((...(((......)))....((((((.(((....))).....(((.(((((....))))).)))........))))))..............))----)))). ( -30.80)
>DroAna_CAF1 15321 102 + 1
AAACAAGUAGUUGAUUCUUCGCCACGGCAGGCUCAAUCUAUUGCCAACCUACUCAUGCGAAUGCGAAACAGUUGAGAUGUUUGAUAGCAAAA-AU-AGGCUA----UA---
(((((..((..((.((((((((...((..(((..........)))..)).......)))))...))).))..))...))))).(((((....-..-..))))----).--- ( -18.70)
>consensus
AAACAAAUAAAGGAUGCAUCACCCACAAGGGCUCAGGCUAUUGCCAAACUGCUCCUGCGCAUGCGCAGCAGCUGAGAAUCGAGCUUGUAAAUCAUAUGGCUA____UUUGC
................(((.........((((((.(((....))).....(((.(((((....))))).)))........)))))).........)))............. (-17.45 = -18.37 +   0.92)

alignment

secondary structure

dotplot

Window 3

Location	4,561,263 – 4,561,374
Length	111
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	81.05
Mean single sequence MFE	-34.90
Consensus MFE	-18.07
Energy contribution	-18.18
Covariance contribution	0.12
Combinations/Pair	1.22
Mean z-score	-2.74
Structure conservation index	0.52
SVM decision value	0.66
SVM RNA-class probability	0.814534
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4561263 111 - 27905053
GCAAAUAAAUAACCAUAGGAUUUACAAGCUCGAUUGUCAGCUGCUGCGCACGCGCAGUAGCAGUUUGGCAAUAGUUUGAGCCCUUAUGGGUGAUGCAUCCUUUAUUUGCUU
((((((((........(((((...((((((..((((((((((((((((....)))))))))....))))))))))))).((((....)))).....))))))))))))).. ( -44.20)
>DroSec_CAF1 18138 107 - 1
GCAAA----UAACCAUAGGAUUUACAAGCUCGAUUCUCAGCUGCUGCGCAUGCGCAGGAGCAGUUUGGCAAUAGCCUGAGCCCUUGUGGGAGAUGCAUCCUUUAUUUGUUU
(((((----(((....(((((......((((....(((((((.(((((....))))).))).....(((....)))))))(((....))).)).))))))))))))))).. ( -36.30)
>DroSim_CAF1 18838 107 - 1
GCAUA----UAACCAUUGGAUUUACAAGCUCGAUUCUCAGCUGCUGCGCAUGCGCAGGAGCAGUUUGGCAAUAGCCUGAGCCCUUGUGGGAGAUGCAUCCUUUAUUUGUUU
((((.----...((((.((........(((((.......(((.(((((....))))).))).....(((....))))))))))..))))...))))............... ( -34.60)
>DroEre_CAF1 18579 107 - 1
GCAAA----UAGCCAUAUGAUUUACAAGCUCGAUUCUCAGCUGCUGCGCAUGCGCAGGAGCAGUUUGGCAAUAGCCUGAGCCCUAGUGGGUGAUACAUCCUUUAUUUGUUU
(((((----(((....(((..((((..(((((.......(((.(((((....))))).))).....(((....))))))))((....))))))..)))...)))))))).. ( -34.10)
>DroYak_CAF1 18373 107 - 1
GCAAA----UAGCCAUAUGAUUUACAAGCUCGAUUCUCAGCUGCUGCGCAUGCGCAGUAGCAAUUUGGCAAUAGCCUGAGCUCUUGUGAUUGAUACAUCCUUUAUUUGUUU
(((((----(((...(((.(.(((((((((((.......(((((((((....))))))))).....(((....)))))))))..))))).).)))......)))))))).. ( -36.80)
>DroAna_CAF1 15321 102 - 1
---UA----UAGCCU-AU-UUUUGCUAUCAAACAUCUCAACUGUUUCGCAUUCGCAUGAGUAGGUUGGCAAUAGAUUGAGCCUGCCGUGGCGAAGAAUCAACUACUUGUUU
---..----((((((-((-((.(((.((((((((.......))))).).))..))).))))))))))(((((((.((((..((((....))..))..))))))).)))).. ( -23.40)
>consensus
GCAAA____UAACCAUAGGAUUUACAAGCUCGAUUCUCAGCUGCUGCGCAUGCGCAGGAGCAGUUUGGCAAUAGCCUGAGCCCUUGUGGGUGAUGCAUCCUUUAUUUGUUU
...................................(((((((.(((((....))))).))).....(((....)))))))(((....)))..................... (-18.07 = -18.18 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:18 2006