Locus 874

Sequence ID	2R_DroMel_CAF1
Location	4,027,000 – 4,027,145
Length	145
Max. P	0.892378

overview

Window 3

Location	4,027,000 – 4,027,116
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.36
Mean single sequence MFE	-32.33
Consensus MFE	-23.89
Energy contribution	-25.20
Covariance contribution	1.31
Combinations/Pair	1.09
Mean z-score	-2.04
Structure conservation index	0.74
SVM decision value	0.11
SVM RNA-class probability	0.588655
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4027000 116 + 20766785
AGGAAUAAACGAACAUAAAAUUACAAAAUGUCAGCAAGUC----UGUGAAAUGAAAUAUCCUGUGGCUGCAGGACUGCGGUAACUGACAAUCAGCUCACACACCUGCUUGCUUAUUUUGU
......................((((((((..(((((((.----(((((..(((....((..((.((((((....)))))).)).))...)))..))))).....))))))))))))))) ( -29.20)
>DroSec_CAF1 9794 120 + 1
AGAAAUAAACGAACAUAAAAUUACAAAAUGUCAGCAAGUCGGGCUGGGAAAUGGAAUAUCCUGUGGCUGCAGGACUGCGCCAACUGACAAUCAGCUCACACACCUGCUUGCUUAUUUUGU
......................((((((((..((((((.((((.((((...(((..((((((((....)))))).))..))).(((.....)))))))....)))))))))))))))))) ( -33.30)
>DroSim_CAF1 11858 120 + 1
AGAAAUAAACGAACAUAAAAUUACAAAAUGUCAGCAAGUCGGGCUGGGAAAUGGAAUAUCCUGUGGCUGCAGGACUGCGCCAACUGACAAUCAGCUCACACACCUGCUUGCUUAUUUUGU
......................((((((((..((((((.((((.((((...(((..((((((((....)))))).))..))).(((.....)))))))....)))))))))))))))))) ( -33.30)
>DroEre_CAF1 8914 120 + 1
AGGAAUAAACGAGCAUAAAAUUACAAAAUGUCAGCAAGCCGGGCUGGGAAAUUGAAUAUCCUGUGGCUGCAGGACUGCGGGAAAUGACAAUCAGCUCGCACACCUGAUUGCUUACAUUGU
..........................(((((.(((((..((((.((............((((((....)))))).((((((...((.....)).)))))))))))).))))).))))).. ( -33.50)
>consensus
AGAAAUAAACGAACAUAAAAUUACAAAAUGUCAGCAAGUCGGGCUGGGAAAUGGAAUAUCCUGUGGCUGCAGGACUGCGCCAACUGACAAUCAGCUCACACACCUGCUUGCUUAUUUUGU
......................((((((((..(((((((.((..((.((..(((....((((((....)))))).....))).(((.....))).)).))..)).))))))))))))))) (-23.89 = -25.20 +   1.31)

alignment

secondary structure

dotplot

Window 4

Location	4,027,000 – 4,027,116
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.36
Mean single sequence MFE	-33.27
Consensus MFE	-27.71
Energy contribution	-29.53
Covariance contribution	1.81
Combinations/Pair	1.03
Mean z-score	-2.02
Structure conservation index	0.83
SVM decision value	0.85
SVM RNA-class probability	0.866863
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4027000 116 - 20766785
ACAAAAUAAGCAAGCAGGUGUGUGAGCUGAUUGUCAGUUACCGCAGUCCUGCAGCCACAGGAUAUUUCAUUUCACA----GACUUGCUGACAUUUUGUAAUUUUAUGUUCGUUUAUUCCU
....(((((((.(((((((.(((((((((.....)))).......((((((......))))))........)))))----.)))))))(((((...........))))).)))))))... ( -34.00)
>DroSec_CAF1 9794 120 - 1
ACAAAAUAAGCAAGCAGGUGUGUGAGCUGAUUGUCAGUUGGCGCAGUCCUGCAGCCACAGGAUAUUCCAUUUCCCAGCCCGACUUGCUGACAUUUUGUAAUUUUAUGUUCGUUUAUUUCU
(((((((.(((((((.(((((((.(((((.....))))).)))).((((((......)))))).............))).).))))))...)))))))...................... ( -36.60)
>DroSim_CAF1 11858 120 - 1
ACAAAAUAAGCAAGCAGGUGUGUGAGCUGAUUGUCAGUUGGCGCAGUCCUGCAGCCACAGGAUAUUCCAUUUCCCAGCCCGACUUGCUGACAUUUUGUAAUUUUAUGUUCGUUUAUUUCU
(((((((.(((((((.(((((((.(((((.....))))).)))).((((((......)))))).............))).).))))))...)))))))...................... ( -36.60)
>DroEre_CAF1 8914 120 - 1
ACAAUGUAAGCAAUCAGGUGUGCGAGCUGAUUGUCAUUUCCCGCAGUCCUGCAGCCACAGGAUAUUCAAUUUCCCAGCCCGGCUUGCUGACAUUUUGUAAUUUUAUGCUCGUUUAUUCCU
..(((((.(((((((.((((((.(((.((.....)).))).))).((((((......)))))).............))).)).))))).))))).......................... ( -25.90)
>consensus
ACAAAAUAAGCAAGCAGGUGUGUGAGCUGAUUGUCAGUUGCCGCAGUCCUGCAGCCACAGGAUAUUCCAUUUCCCAGCCCGACUUGCUGACAUUUUGUAAUUUUAUGUUCGUUUAUUCCU
(((((((.(((((((.(((((((.(((((.....))))).)))).((((((......)))))).............))).).))))))...)))))))...................... (-27.71 = -29.53 +   1.81)

alignment

secondary structure

dotplot

Window 5

Location	4,027,040 – 4,027,145
Length	105
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.59
Mean single sequence MFE	-30.80
Consensus MFE	-25.30
Energy contribution	-27.17
Covariance contribution	1.88
Combinations/Pair	1.04
Mean z-score	-1.97
Structure conservation index	0.82
SVM decision value	0.97
SVM RNA-class probability	0.892378
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4027040 105 - 20766785
AAAAAGGAAAUGGUCCCAUAAUUUU-----------AAGCACAAAAUAAGCAAGCAGGUGUGUGAGCUGAUUGUCAGUUACCGCAGUCCUGCAGCCACAGGAUAUUUCAUUUCACA----
......((((((((((.........-----------..((.........))..(((((((((..(((((.....)))))..))))..))))).......))))....))))))...---- ( -27.30)
>DroSec_CAF1 9834 109 - 1
AAAAAGGAAAUGGUCCCAUAAUUUU-----------UAGCACAAAAUAAGCAAGCAGGUGUGUGAGCUGAUUGUCAGUUGGCGCAGUCCUGCAGCCACAGGAUAUUCCAUUUCCCAGCCC
.....(((((((((((.........-----------..((.........))..((((((((((.(((((.....))))).)))))..))))).......)))....))))))))...... ( -35.60)
>DroSim_CAF1 11898 109 - 1
AAAAAGGAAAUGGUCCCAUAAUUUU-----------UAGCACAAAAUAAGCAAGCAGGUGUGUGAGCUGAUUGUCAGUUGGCGCAGUCCUGCAGCCACAGGAUAUUCCAUUUCCCAGCCC
.....(((((((((((.........-----------..((.........))..((((((((((.(((((.....))))).)))))..))))).......)))....))))))))...... ( -35.60)
>DroEre_CAF1 8954 120 - 1
AAGCAGGAAACGUUCCCCUCAUUUUUAGCCUCAUUUUAGCACAAUGUAAGCAAUCAGGUGUGCGAGCUGAUUGUCAUUUCCCGCAGUCCUGCAGCCACAGGAUAUUCAAUUUCCCAGCCC
..((.(((((.................((.........)).........((((((((.(.....).))))))))..))))).)).((((((......))))))................. ( -24.70)
>consensus
AAAAAGGAAAUGGUCCCAUAAUUUU___________UAGCACAAAAUAAGCAAGCAGGUGUGUGAGCUGAUUGUCAGUUGCCGCAGUCCUGCAGCCACAGGAUAUUCCAUUUCCCAGCCC
.....(((((((((((......................((.........))..((((((((((.(((((.....))))).)))))..))))).......)))....))))))))...... (-25.30 = -27.17 +   1.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:34 2006