Locus 8651

Sequence ID	3L_DroMel_CAF1
Location	22,452,395 – 22,452,506
Length	111
Max. P	0.744878

overview

Window 8

Location	22,452,395 – 22,452,506
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.81
Mean single sequence MFE	-20.48
Consensus MFE	-13.60
Energy contribution	-14.52
Covariance contribution	0.92
Combinations/Pair	1.09
Mean z-score	-1.86
Structure conservation index	0.66
SVM decision value	0.10
SVM RNA-class probability	0.583815
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22452395 111 + 23771897
CCGCAAUUAGUUAGGCCCCAGCAGACAAAUCUGCAAAGCAAGCAAA-CAAACUGCGAACUGCU------AAACCAUAAAA-CCAGAAAAGUCGUCCAACUUUUCCAGCA-AACGACCCAA
..((.........((.....(((((....)))))..((((.(((..-.....)))....))))------...))......-...(((((((......)))))))..)).-.......... ( -21.10)
>DroPse_CAF1 17238 110 + 1
CCACAAUUA----------AGCAGACAAGUCCCCGAAGCAAAUAAAAGAAGCUCUGGAGUCCGUCCUGCAAUCCAUGAAGUCCGUGAAAGUCGGUCAACUUUUUUAGCGCUACGAGCCAA
.........----------.((.((....))..((.(((...(((((((.((...(((.....))).))..........(.((((....).))).)...)))))))..))).)).))... ( -17.50)
>DroSec_CAF1 3751 111 + 1
CCGCAAUUAGUUAGGCCCCAGCAGACAAAUCUGCAAAGCAAGCAAA-CAAACUGCGAACUGCU------AAACCAUAAAA-CCAGAAAAGUCGUCCAACUUUUCUAGCA-AACGACCCAA
..((.........((.....(((((....)))))..((((.(((..-.....)))....))))------...))......-..((((((((......)))))))).)).-.......... ( -22.70)
>DroSim_CAF1 3755 111 + 1
CCGCAAUUAGUUAGGCCCCAGCAGACAAAUCUGCAAAGCAAGCAAA-CAAACUGCGAACUGCU------AAACCAUAAAA-CCAGAAAAGUCGUCCAACUUUUCCAGCA-AACGACCCAA
..((.........((.....(((((....)))))..((((.(((..-.....)))....))))------...))......-...(((((((......)))))))..)).-.......... ( -21.10)
>DroEre_CAF1 8062 100 + 1
CCGCAAUUAGUUAGGCCCCAGCAGACAAAUCUGCAAAGCAAGCAAA-CAAACUGCGAAAUGCU------AAACCAUAAAA-CCAGAAAAGUCGUCCAACUUUUCCAGC------------
..((.........((.....(((((....)))))..((((.(((..-.....)))....))))------...))......-...(((((((......)))))))..))------------ ( -19.40)
>DroYak_CAF1 9260 111 + 1
CCGCAAUUAGUUAGGCCCCAGCAGACAAAUCUGCAAAGCAAGCAAA-CAAACUGCGAACUGCU------AAACCAUAAAA-CCAGAAAAGUCGUCCAACUUUUCCAGCA-AACGACCCAA
..((.........((.....(((((....)))))..((((.(((..-.....)))....))))------...))......-...(((((((......)))))))..)).-.......... ( -21.10)
>consensus
CCGCAAUUAGUUAGGCCCCAGCAGACAAAUCUGCAAAGCAAGCAAA_CAAACUGCGAACUGCU______AAACCAUAAAA_CCAGAAAAGUCGUCCAACUUUUCCAGCA_AACGACCCAA
..((.........((.....(((((....)))))...(((.(((........)))....)))..........))..........(((((((......)))))))..))............ (-13.60 = -14.52 +   0.92)

alignment

secondary structure

dotplot

Window 9

Location	22,452,395 – 22,452,506
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.81
Mean single sequence MFE	-34.72
Consensus MFE	-22.50
Energy contribution	-23.50
Covariance contribution	1.00
Combinations/Pair	1.14
Mean z-score	-2.53
Structure conservation index	0.65
SVM decision value	0.46
SVM RNA-class probability	0.744878
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22452395 111 - 23771897
UUGGGUCGUU-UGCUGGAAAAGUUGGACGACUUUUCUGG-UUUUAUGGUUU------AGCAGUUCGCAGUUUG-UUUGCUUGCUUUGCAGAUUUGUCUGCUGGGGCCUAACUAAUUGCGG
((((..(((.-.((..((((((((....))))))))..)-)...)))..))------)).....(((((((.(-((.....((((((((((....))))).)))))..))).))))))). ( -37.30)
>DroPse_CAF1 17238 110 - 1
UUGGCUCGUAGCGCUAAAAAAGUUGACCGACUUUCACGGACUUCAUGGAUUGCAGGACGGACUCCAGAGCUUCUUUUAUUUGCUUCGGGGACUUGUCUGCU----------UAAUUGUGG
(((((.......))))).((((((....))))))(((((.((....))...(((((..((.((((..(((...........)))..)))).))..))))).----------...))))). ( -25.90)
>DroSec_CAF1 3751 111 - 1
UUGGGUCGUU-UGCUAGAAAAGUUGGACGACUUUUCUGG-UUUUAUGGUUU------AGCAGUUCGCAGUUUG-UUUGCUUGCUUUGCAGAUUUGUCUGCUGGGGCCUAACUAAUUGCGG
((((..(((.-.((((((((((((....)))))))))))-)...)))..))------)).....(((((((.(-((.....((((((((((....))))).)))))..))).))))))). ( -38.30)
>DroSim_CAF1 3755 111 - 1
UUGGGUCGUU-UGCUGGAAAAGUUGGACGACUUUUCUGG-UUUUAUGGUUU------AGCAGUUCGCAGUUUG-UUUGCUUGCUUUGCAGAUUUGUCUGCUGGGGCCUAACUAAUUGCGG
((((..(((.-.((..((((((((....))))))))..)-)...)))..))------)).....(((((((.(-((.....((((((((((....))))).)))))..))).))))))). ( -37.30)
>DroEre_CAF1 8062 100 - 1
------------GCUGGAAAAGUUGGACGACUUUUCUGG-UUUUAUGGUUU------AGCAUUUCGCAGUUUG-UUUGCUUGCUUUGCAGAUUUGUCUGCUGGGGCCUAACUAAUUGCGG
------------((..((((((((....))))))))..)-)..........------.......(((((((.(-((.....((((((((((....))))).)))))..))).))))))). ( -32.20)
>DroYak_CAF1 9260 111 - 1
UUGGGUCGUU-UGCUGGAAAAGUUGGACGACUUUUCUGG-UUUUAUGGUUU------AGCAGUUCGCAGUUUG-UUUGCUUGCUUUGCAGAUUUGUCUGCUGGGGCCUAACUAAUUGCGG
((((..(((.-.((..((((((((....))))))))..)-)...)))..))------)).....(((((((.(-((.....((((((((((....))))).)))))..))).))))))). ( -37.30)
>consensus
UUGGGUCGUU_UGCUGGAAAAGUUGGACGACUUUUCUGG_UUUUAUGGUUU______AGCAGUUCGCAGUUUG_UUUGCUUGCUUUGCAGAUUUGUCUGCUGGGGCCUAACUAAUUGCGG
.............(((((((((((....)))))))))))........................((((((((......((((.....(((((....)))))..))))......)))))))) (-22.50 = -23.50 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:21:25 2006