Locus 3759

Sequence ID	3L_DroMel_CAF1
Location	10,883,150 – 10,883,273
Length	123
Max. P	0.867411

overview

Window 5

Location	10,883,150 – 10,883,241
Length	91
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	76.97
Mean single sequence MFE	-24.53
Consensus MFE	-10.52
Energy contribution	-11.83
Covariance contribution	1.31
Combinations/Pair	1.14
Mean z-score	-2.42
Structure conservation index	0.43
SVM decision value	0.85
SVM RNA-class probability	0.867411
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10883150 91 - 23771897
------CAUGGUACCCGUUGGCCAU-----UGGCCGAUCUAAGGCUGAAUGGCUGAAUGGUUGAAUUAACAAAAUCAUAAAGCAAAUAGUCCGACCAUAUCG
------.(((((....(((((((..-----.)))))))....(((((....(((..((((((..........))))))..)))...)))))..))))).... ( -25.00)
>DroSec_CAF1 15508 90 - 1
------CAUGGUACACA-UGGCCAU-----UGGCCGAUCUAAGGCUGAAUGGCUGAAUGGUUGAAUUAACAAAAUCAUAAAGCAAAUAGUCCGACCAUAUCG
------((((.....))-))(((((-----(((((.......)))).)))))).(((((((((.((((..................)))).))))))).)). ( -25.67)
>DroSim_CAF1 11491 90 - 1
------CAUGGUACCCA-UGGCCAU-----UGGCCGAUCUAAGGCUGAAUGGCUGAAUGGUUGAAUUAACAAAAUCAUAAAGCAAAUAGUCCGACCAUAUCG
------(((((...)))-))(((((-----(((((.......)))).)))))).(((((((((.((((..................)))).))))))).)). ( -26.47)
>DroEre_CAF1 10793 80 - 1
------CAUGGUC--------CCGUGGCCAUGGCCGAUCUAAGGCUCAAUGGCAG--------AAUUAACAAAAUCAUAAAGCAAAUAGUCGGACCAUAUCG
------.((((((--------(....(((((((((.......))))..))))).(--------(.((....)).))...............))))))).... ( -22.70)
>DroYak_CAF1 12407 93 - 1
GAUAGCCAUGGUCCGCA-UGGCCAUGUCCAUGGCCAAUCUAAGGCUCAAUGGCAG--------AAUUAACAAAAUCAUAAAGCAAAUAGUCGGACCAUAUCG
((((....((((((((.-(((((((....))))))).......(((..((((...--------...........))))..))).....).))))))))))). ( -28.84)
>DroAna_CAF1 5138 83 - 1
------CAGACUCCAAG-U-CCCAGCUCCGACUCCGAUCUGAGGCUGAAUGGCUG--------AAUUAACAAAAUCAUAAAGCAAAUAGUCGGACCUGA---
------..(((.....)-)-).(((.(((((((.(.......)(((..(((..(.--------.........)..)))..)))....))))))).))).--- ( -18.50)
>consensus
______CAUGGUACACA_UGGCCAU_____UGGCCGAUCUAAGGCUGAAUGGCUG________AAUUAACAAAAUCAUAAAGCAAAUAGUCCGACCAUAUCG
.......(((((.......(((((......)))))((.(((..(((..((((......................))))..)))...)))))..))))).... (-10.52 = -11.83 +   1.31)

alignment

secondary structure

dotplot

Window 6

Location	10,883,175 – 10,883,273
Length	98
Sequences	4
Columns	103
Reading direction	reverse
Mean pairwise identity	77.03
Mean single sequence MFE	-26.57
Consensus MFE	-11.89
Energy contribution	-13.58
Covariance contribution	1.69
Combinations/Pair	1.10
Mean z-score	-2.69
Structure conservation index	0.45
SVM decision value	0.64
SVM RNA-class probability	0.808553
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10883175 98 - 23771897
UCCCAUAUCCCAUUCCCACAGACGCCAAUCGCCAUGGUACCCGUUGGCCAU-----UGGCCGAUCUAAGGCUGAAUGGCUGAAUGGUUGAAUUAACAAAAUCA
..((((.((((((((((..((((((((((.(((((((...))).)))).))-----))).)).)))..))..))))))..))))))................. ( -29.00)
>DroSec_CAF1 15533 90 - 1
UC-------CCAUUCCCACAGACGCCAAUCGUCAUGGUACACA-UGGCCAU-----UGGCCGAUCUAAGGCUGAAUGGCUGAAUGGUUGAAUUAACAAAAUCA
..-------((((((....((((((((((.((((((.....))-)))).))-----))).)).)))..((((....))))))))))................. ( -27.90)
>DroSim_CAF1 11516 90 - 1
UC-------CCAUUCCCACAGACGCCAAUCGCCAUGGUACCCA-UGGCCAU-----UGGCCGAUCUAAGGCUGAAUGGCUGAAUGGUUGAAUUAACAAAAUCA
..-------((((((....((((((((((.(((((((...)))-)))).))-----))).)).)))..((((....))))))))))................. ( -31.40)
>DroAna_CAF1 5160 86 - 1
UC-------UCUUUCCCACAGACUCCCAGUUGCAGACUCCAAG-U-CCCAGCUCCGACUCCGAUCUGAGGCUGAAUGGCUG--------AAUUAACAAAAUCA
..-------.........(((.((..((((..((((.((..((-(-(........))))..))))))..))))...)))))--------.............. ( -18.00)
>consensus
UC_______CCAUUCCCACAGACGCCAAUCGCCAUGGUACACA_UGGCCAU_____UGGCCGAUCUAAGGCUGAAUGGCUGAAUGGUUGAAUUAACAAAAUCA
.........((((((((..(((.((((.......))))......((((((......)))))).)))..))..))))))......................... (-11.89 = -13.58 +   1.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:00 2006