Locus 7136

Sequence ID	3L_DroMel_CAF1
Location	19,181,566 – 19,181,679
Length	113
Max. P	0.714902

overview

Window 7

Location	19,181,566 – 19,181,679
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.84
Mean single sequence MFE	-39.62
Consensus MFE	-34.28
Energy contribution	-35.64
Covariance contribution	1.36
Combinations/Pair	1.10
Mean z-score	-1.40
Structure conservation index	0.87
SVM decision value	0.38
SVM RNA-class probability	0.714902
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19181566 113 + 23771897
CCGGACACACCUGAGAGUCCUGGCAAAGGAUGGGCCGAGGGAUAGGAUAUAC------UCGCACAGCAAAUAUCUGGCGCACAUCGUGUCUUCCCGCCCCUCAGCCCAAAAC-UCUUCCC
..((.....)).(((((((((.....))))(((((.(((((...(((.((((------.(((.(((.......))))))......))))..)))...))))).)))))...)-))))... ( -36.70)
>DroSec_CAF1 10109 113 + 1
CCGGACACACCUGAGAGUCCUGGCGAAGGAUGGGCCGAGGGAUAGGAUAUAC------UCGCACAGCAAAUAUCUGGCGCACAUCGUGUCUUCCCGCCCCUCAGCCCACAAC-UCGUCCU
..((((..........(((((.....)))))((((.(((((...(((.((((------.(((.(((.......))))))......))))..)))...))))).)))).....-..)))). ( -39.60)
>DroSim_CAF1 13228 113 + 1
CCGGACACACCUGAGAGUCCUGGCGAAGGAUGGGCCGAGGGAUGGGAUAUAC------UCGCACAGCAAAUAUCUGGCGCACAUCGUGUCUUCCCGCCCCUCAGCCCACAAC-UCGUCCU
..((((..........(((((.....)))))((((.(((((.(((((.((((------.(((.(((.......))))))......))))..))))).))))).)))).....-..)))). ( -45.20)
>DroEre_CAF1 12837 119 + 1
CCGGACACACCUGAGAGUCCUGGCGAAGGAUGGGCCGC-GGAUAGGAUAUACUCGUACUCGUUCAGCAAAUAUCUGGCGCACAUCGCGUCUUCCUGCCGCUCCGCCCUCGACAUCGUCCU
..((((..........(((((.....)))))((((.((-((.(((((......((....))..............(((((.....))))).)))))))))...))))........)))). ( -39.00)
>DroYak_CAF1 33734 112 + 1
CCGGACACACCUGAGAGUCCUGGCGAAGGAUGGGCCGAGGGAUAGGAUAUAC------UCGUUCAGCAAAUAUCUGGCGCACAUCGCGUCUUCCUUCCGCUCC--CCUCGACAUCGUCCU
..((((.....((((.(((((.....)))))((((.((((((..((((((..------.(.....)...))))))(((((.....))))).)))))).)))).--.)))).....)))). ( -37.60)
>consensus
CCGGACACACCUGAGAGUCCUGGCGAAGGAUGGGCCGAGGGAUAGGAUAUAC______UCGCACAGCAAAUAUCUGGCGCACAUCGUGUCUUCCCGCCCCUCAGCCCACAAC_UCGUCCU
..((((..........(((((.....)))))((((.(((((.(((((.............((...))........(((((.....))))).))))).))))).))))........)))). (-34.28 = -35.64 +   1.36)

alignment

secondary structure

dotplot

Window 8

Location	19,181,566 – 19,181,679
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.84
Mean single sequence MFE	-46.52
Consensus MFE	-37.48
Energy contribution	-39.72
Covariance contribution	2.24
Combinations/Pair	1.09
Mean z-score	-1.49
Structure conservation index	0.81
SVM decision value	0.26
SVM RNA-class probability	0.656079
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19181566 113 - 23771897
GGGAAGA-GUUUUGGGCUGAGGGGCGGGAAGACACGAUGUGCGCCAGAUAUUUGCUGUGCGA------GUAUAUCCUAUCCCUCGGCCCAUCCUUUGCCAGGACUCUCAGGUGUGUCCGG
.((.(((-(...(((((((((((..((((...(((...)))((((((.......))).))).------.....))))..)))))))))))..)))).)).((((.(......).)))).. ( -49.10)
>DroSec_CAF1 10109 113 - 1
AGGACGA-GUUGUGGGCUGAGGGGCGGGAAGACACGAUGUGCGCCAGAUAUUUGCUGUGCGA------GUAUAUCCUAUCCCUCGGCCCAUCCUUCGCCAGGACUCUCAGGUGUGUCCGG
.((.(((-(..((((((((((((..((((...(((...)))((((((.......))).))).------.....))))..))))))))))))..)))))).((((.(......).)))).. ( -52.90)
>DroSim_CAF1 13228 113 - 1
AGGACGA-GUUGUGGGCUGAGGGGCGGGAAGACACGAUGUGCGCCAGAUAUUUGCUGUGCGA------GUAUAUCCCAUCCCUCGGCCCAUCCUUCGCCAGGACUCUCAGGUGUGUCCGG
.((.(((-(..((((((((((((..((((...(((...)))((((((.......))).))).------.....))))..))))))))))))..)))))).((((.(......).)))).. ( -54.10)
>DroEre_CAF1 12837 119 - 1
AGGACGAUGUCGAGGGCGGAGCGGCAGGAAGACGCGAUGUGCGCCAGAUAUUUGCUGAACGAGUACGAGUAUAUCCUAUCC-GCGGCCCAUCCUUCGCCAGGACUCUCAGGUGUGUCCGG
.((((.((..((((((.((.((.((.(((....(.(((((((....(.((((((.....)))))))..))))))))..)))-)).)))).((((.....))))))))).)..)))))).. ( -38.90)
>DroYak_CAF1 33734 112 - 1
AGGACGAUGUCGAGG--GGAGCGGAAGGAAGACGCGAUGUGCGCCAGAUAUUUGCUGAACGA------GUAUAUCCUAUCCCUCGGCCCAUCCUUCGCCAGGACUCUCAGGUGUGUCCGG
.((((((((((((((--((.(((.........)))(((((((..(((.......))).....------)))))))...)))))))))..)))...((((.((....)).)))).)))).. ( -37.60)
>consensus
AGGACGA_GUUGUGGGCUGAGGGGCGGGAAGACACGAUGUGCGCCAGAUAUUUGCUGUGCGA______GUAUAUCCUAUCCCUCGGCCCAUCCUUCGCCAGGACUCUCAGGUGUGUCCGG
.((.(((....((((((((((((..((((..((........((((((.......))).))).......))...))))..))))))))))))...))))).((((.(......).)))).. (-37.48 = -39.72 +   2.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:59 2006