Locus 8621

Sequence ID	3L_DroMel_CAF1
Location	22,428,501 – 22,428,700
Length	199
Max. P	0.943620

overview

Window 5

Location	22,428,501 – 22,428,620
Length	119
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	95.66
Mean single sequence MFE	-40.20
Consensus MFE	-37.75
Energy contribution	-37.62
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-1.44
Structure conservation index	0.94
SVM decision value	0.06
SVM RNA-class probability	0.564221
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22428501 119 - 23771897
UAAAUUUGCAUUUAAAUGUGCCAUGGCGAACGGCCCGGGGAACGGGCGGCGGUUCUUCGUGUCUGAUUGAAGGCCGCUCGGCCUCAGGAGGGCCUGAAAAAGAGCUGGAAUUAUAAUAA
..(((((((((......)))).........(.(((((.....))))).)((((((((((.((((..((((.((((....))))))))..)))).)))...))))))))))))....... ( -41.40)
>DroSec_CAF1 203 119 - 1
UAAAUUUGCAUUCAAAUGUGUCAUGGCGAGCGGUCCGGGGAACGGGCGCCGGUUCUUCGUGUCUGAUUGAAGGCCGCUCGGCCUCAGGAGGGCCUGAAAAAGAGCUGGAAUUAUAAUAA
..(((((((((......))))...(((((((((((((((((((.(....).))))))))..((.....)).))))))))(((((.....))))).........))).)))))....... ( -40.20)
>DroSim_CAF1 5109 119 - 1
UAAAUUUGCAUUCAAAUGUGUCAUGGCGAGCGGUCCGGGGAACGGGCGCCGGUUCUUCGUGUCUGAUUGAAGGCCGCUCGGCCUCAGGAGGGCCUGAAAAAGAGCUGGAAUUAUAAUAA
..(((((((((......))))...(((((((((((((((((((.(....).))))))))..((.....)).))))))))(((((.....))))).........))).)))))....... ( -40.20)
>DroYak_CAF1 40298 119 - 1
UAAAUUUGCAUUCAAAUGUGUCAUGGCGAAUGGUCCGGGGAACGGGCGCCGGUUCUUCGUGUCUGAUUGAAGGCCGCUCGGCCUGAGAAGGGCUUGAAAAAGAGCUGGAAUUAUAAUAG
...((((((...((....)).....)))))).(((((.....))))).(((((((((((.((((..((..(((((....)))))..)).)))).)))...))))))))........... ( -39.00)
>consensus
UAAAUUUGCAUUCAAAUGUGUCAUGGCGAACGGUCCGGGGAACGGGCGCCGGUUCUUCGUGUCUGAUUGAAGGCCGCUCGGCCUCAGGAGGGCCUGAAAAAGAGCUGGAAUUAUAAUAA
....(((((...((....)).....)))))..(((((.....))))).(((((((((((.((((..((((.((((....))))))))..)))).)))...))))))))........... (-37.75 = -37.62 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	22,428,540 – 22,428,660
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.50
Mean single sequence MFE	-41.72
Consensus MFE	-32.84
Energy contribution	-34.52
Covariance contribution	1.68
Combinations/Pair	1.10
Mean z-score	-2.17
Structure conservation index	0.79
SVM decision value	1.34
SVM RNA-class probability	0.943620
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22428540 120 - 23771897
CCCGUUGGUUUUUGUUGUUAGCACAUUGACACGUUGUGCAUAAAUUUGCAUUUAAAUGUGCCAUGGCGAACGGCCCGGGGAACGGGCGGCGGUUCUUCGUGUCUGAUUGAAGGCCGCUCG
((((..(((((((((..(..(((((((........(((((......)))))...))))))).)..))))).))))))))...((((((((....(((((........))))))))))))) ( -45.40)
>DroSec_CAF1 242 120 - 1
CCCGUUUGUUUUUGUUGUUAGCACAUUGACACGUUUUGCAUAAAUUUGCAUUCAAAUGUGUCAUGGCGAGCGGUCCGGGGAACGGGCGCCGGUUCUUCGUGUCUGAUUGAAGGCCGCUCG
....................((.(((.(((((((((((((......))))...))))))))))))))((((((((((((((((.(....).))))))))..((.....)).)))))))). ( -45.80)
>DroSim_CAF1 5148 120 - 1
CCCGUUUGUUUUUGUUGUUAGCACAUUGACACGUUUUGCAUAAAUUUGCAUUCAAAUGUGUCAUGGCGAGCGGUCCGGGGAACGGGCGCCGGUUCUUCGUGUCUGAUUGAAGGCCGCUCG
....................((.(((.(((((((((((((......))))...))))))))))))))((((((((((((((((.(....).))))))))..((.....)).)))))))). ( -45.80)
>DroEre_CAF1 6310 99 - 1
CCCGUUUGUUUUUGUUGUUAGCACAUUGACACGUUUUGCAUAAAUUUGCAUUCAAAUGUGUCAUGGCGAACGCUGCAGGGAACGGGCGCCGCUCCUUCG---------------------
(((((((.((...((.(((.((.(((.(((((((((((((......))))...)))))))))))))).)))))...)).))))))).............--------------------- ( -31.90)
>DroYak_CAF1 40337 120 - 1
CCCGUUUGUUUUUGUUGUUAGCACAUUGACACGUUUUGCAUAAAUUUGCAUUCAAAUGUGUCAUGGCGAAUGGUCCGGGGAACGGGCGCCGGUUCUUCGUGUCUGAUUGAAGGCCGCUCG
(((((((.((...(..(((.((.(((.(((((((((((((......))))...)))))))))))))).)))..)..)).))))))).((.(((.(((((........))))))))))... ( -39.70)
>consensus
CCCGUUUGUUUUUGUUGUUAGCACAUUGACACGUUUUGCAUAAAUUUGCAUUCAAAUGUGUCAUGGCGAACGGUCCGGGGAACGGGCGCCGGUUCUUCGUGUCUGAUUGAAGGCCGCUCG
(((((((.((...(..(((.((.(((.(((((((((((((......))))...)))))))))))))).)))..)..)).)))))))...((((.(((((........))))))))).... (-32.84 = -34.52 +   1.68)

alignment

secondary structure

dotplot

Window 7

Location	22,428,580 – 22,428,700
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.83
Mean single sequence MFE	-34.64
Consensus MFE	-28.82
Energy contribution	-29.18
Covariance contribution	0.36
Combinations/Pair	1.15
Mean z-score	-1.30
Structure conservation index	0.83
SVM decision value	-0.01
SVM RNA-class probability	0.529710
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22428580 120 - 23771897
UCUUGCACUUUUUCAGCUUUAGUCACACGUUAGAACGGGACCCGUUGGUUUUUGUUGUUAGCACAUUGACACGUUGUGCAUAAAUUUGCAUUUAAAUGUGCCAUGGCGAACGGCCCGGGG
.......((..((((((...........))).)))..)).((((..(((((((((..(..(((((((........(((((......)))))...))))))).)..))))).)))))))). ( -30.70)
>DroSec_CAF1 282 120 - 1
UCUUGCACUUUUUCAGCUGUAGUCACACGUUAGAGCGGCACCCGUUUGUUUUUGUUGUUAGCACAUUGACACGUUUUGCAUAAAUUUGCAUUCAAAUGUGUCAUGGCGAGCGGUCCGGGG
.((((..........(((((..((........)))))))..((((((((...(((.....)))(((.(((((((((((((......))))...))))))))))))))))))))..)))). ( -33.30)
>DroSim_CAF1 5188 120 - 1
UCUUGCACUUUUUCAGCUUUAGUCACACGUUAGAGCGGCACCCGUUUGUUUUUGUUGUUAGCACAUUGACACGUUUUGCAUAAAUUUGCAUUCAAAUGUGUCAUGGCGAGCGGUCCGGGG
..........(..(.(((((((.(....))))))))((...((((((((...(((.....)))(((.(((((((((((((......))))...)))))))))))))))))))).)))..) ( -34.10)
>DroEre_CAF1 6329 120 - 1
CCCUGCACUUUUUCAGCUUUAGUCACACGUUAGAGCGGCACCCGUUUGUUUUUGUUGUUAGCACAUUGACACGUUUUGCAUAAAUUUGCAUUCAAAUGUGUCAUGGCGAACGCUGCAGGG
(((((((........(((((((.(....))))))))......(((((((...(((.....)))(((.(((((((((((((......))))...))))))))))))))))))).))))))) ( -40.10)
>DroYak_CAF1 40377 120 - 1
UCUUGCACUUUUUCAGCUUGGGUCACACGUUAGAGCAGCACCCGUUUGUUUUUGUUGUUAGCACAUUGACACGUUUUGCAUAAAUUUGCAUUCAAAUGUGUCAUGGCGAAUGGUCCGGGG
................(((((..((..(((((.(((((((............))))))).......((((((((((((((......))))...)))))))))))))))..))..))))). ( -35.00)
>consensus
UCUUGCACUUUUUCAGCUUUAGUCACACGUUAGAGCGGCACCCGUUUGUUUUUGUUGUUAGCACAUUGACACGUUUUGCAUAAAUUUGCAUUCAAAUGUGUCAUGGCGAACGGUCCGGGG
(((((..........(((((((.(....)))))))).....((((((((...(((.....)))(((.(((((((((((((......))))...))))))))))))))))))))..))))) (-28.82 = -29.18 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:35 2006