Locus 5067

Sequence ID	2L_DroMel_CAF1
Location	14,498,918 – 14,499,064
Length	146
Max. P	0.553606

overview

Window 2

Location	14,498,918 – 14,499,026
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.18
Mean single sequence MFE	-35.77
Consensus MFE	-14.90
Energy contribution	-15.22
Covariance contribution	0.31
Combinations/Pair	1.35
Mean z-score	-2.20
Structure conservation index	0.42
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14498918 108 + 22407834
C---GUGGGCUGAUUGGUAAAAUCAG-----GUCACUGGCAGAAAGCC-GUCAGCGGCAAUCG---CCAUACGCAGAUAACUUAUUUAUCGGAAAUGGCUGUUGACAAAUCCGGUAAUGA
.---((((.((((((.....))))))-----.))))((((.((..(((-(....))))..)))---)))................((((((((..((........))..))))))))... ( -36.00)
>DroSec_CAF1 30623 111 + 1
C---GUGGGCUGAUUGGUAAAAUCAG-----GUCACUGGCAGAAAGCC-GUCAGCGGCAAUCGCCGCCAUUCGCAGAUAACUCAUUUAUCGGAAAUGGCUGUUGACAAAUCCGGUAAUGA
.---((((.((((((.....))))))-----.)))).(((.....)))-(((((((((....)))((((((....(((((.....)))))...)))))).)))))).............. ( -40.80)
>DroSim_CAF1 14657 111 + 1
C---GUGGGCUGAUUGGUAAAAUCAG-----GUCACUGGCAGAAAGCC-GUCAGCGGCAAUCGCCGCCAUUCGCAGAUAACUCAUUUAUCGGAAAUGGCUGUUGACAAAUCCGGUAAUGA
.---((((.((((((.....))))))-----.)))).(((.....)))-(((((((((....)))((((((....(((((.....)))))...)))))).)))))).............. ( -40.80)
>DroEre_CAF1 24673 108 + 1
CG----GGACUGAUUGGUAAAAUCAG-----GUCACUGGCAGAAAGCCAGUCGGCGGCAAUCG---GCACUCGCAGAUAACUCAUUUAUCGCAAAUGCUUGUUGACAAAUCCGGUAAUGA
((----((.((((((.....))))))-----(((((((((.....)))))).)))(.((((.(---(((...((.(((((.....)))))))...)))).)))).)...))))....... ( -34.80)
>DroYak_CAF1 19884 111 + 1
CAGCGUGGGCUGAUUGGUAAAAUCAG-----GUCACUGGCAGAAAGCC-GUCAGCGGUAAUCG---CCAUUCGCAGAUAACUCAUUUAUCGGAAAUGCUCGUUGACAAAUCCGGUGAUGA
..((((((.((((((.....))))))-----.))))((((.((..(((-(....))))..)))---)))...)).......(((((.((((((..(((.....).))..))))))))))) ( -37.40)
>DroPer_CAF1 16965 100 + 1
A---GUGUGGUG--UGGUGCUGUGGGUUUCACUGAAUGGCAUGGAAAU-GUCACCAACAAU------------CAGGCAACACA--UAUCGGAAAUUGUCGCUGACAGAGCUGUUAAUGU
.---((((.((.--((((....(((..(((...)))((((((....))-)))))))...))------------)).)).)))).--((.(((...(((((...)))))..))).)).... ( -24.80)
>consensus
C___GUGGGCUGAUUGGUAAAAUCAG_____GUCACUGGCAGAAAGCC_GUCAGCGGCAAUCG___CCAUUCGCAGAUAACUCAUUUAUCGGAAAUGGCUGUUGACAAAUCCGGUAAUGA
........((((((.(((....((((.........))))......))).))))))..........................((((.(((((((..((........))..))))))))))) (-14.90 = -15.22 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	14,498,950 – 14,499,064
Length	114
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.64
Mean single sequence MFE	-29.70
Consensus MFE	-13.84
Energy contribution	-15.07
Covariance contribution	1.23
Combinations/Pair	1.26
Mean z-score	-1.91
Structure conservation index	0.47
SVM decision value	0.04
SVM RNA-class probability	0.553606
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14498950 114 - 22407834
UUUAACGAAUCAUCGAUUAAACGCGAGAUCGUAGA--AAUUCAUUACCGGAUUUGUCAACAGCCAUUUCCGAUAAAUAAGUUAUCUGCGUAUGG---CGAUUGCCGCUGAC-GGCUUUCU
((((((((....))).))))).((.(...((((((--((((..(((.((((..((.(....).))..)))).)))...)))).))))))..).)---)((..((((....)-)))..)). ( -28.40)
>DroSec_CAF1 30655 116 - 1
UUUAACGAAUCAUCGAUUAAACA-GAGAUCGUAGA--AAUUCAUUACCGGAUUUGUCAACAGCCAUUUCCGAUAAAUGAGUUAUCUGCGAAUGGCGGCGAUUGCCGCUGAC-GGCUUUCU
((((((((....))).))))).(-(((((((((((--((((((((..((((..((.(....).))..))))...)))))))).)))))))..((((((....))))))...-...))))) ( -36.20)
>DroSim_CAF1 14689 116 - 1
UUUAACGAAUCAUCGAUUAAACA-GAGAUCGUAGA--AAUUCAUUACCGGAUUUGUCAACAGCCAUUUCCGAUAAAUGAGUUAUCUGCGAAUGGCGGCGAUUGCCGCUGAC-GGCUUUCU
((((((((....))).))))).(-(((((((((((--((((((((..((((..((.(....).))..))))...)))))))).)))))))..((((((....))))))...-...))))) ( -36.20)
>DroEre_CAF1 24704 114 - 1
AUGAACGUAUCAUCGAUUAAACA-CAGAUCGUAGA--AAUUCAUUACCGGAUUUGUCAACAAGCAUUUGCGAUAAAUGAGUUAUCUGCGAGUGC---CGAUUGCCGCCGACUGGCUUUCU
.(((.((......)).)))..((-(...(((((((--((((((((..((.(..(((......)))..).))...)))))))).)))))))))).---.((..((((.....))))..)). ( -26.80)
>DroYak_CAF1 19919 113 - 1
AUUAACGCACAAUCGAUUAAACA-GAGAUCGUAGA--AAUUCAUCACCGGAUUUGUCAACGAGCAUUUCCGAUAAAUGAGUUAUCUGCGAAUGG---CGAUUACCGCUGAC-GGCUUUCU
.....(((.((.((((((.....-..))))(((((--(((((((...((((..(((......)))..))))....))))))).))))))).)))---))....(((....)-))...... ( -29.70)
>DroPer_CAF1 17000 90 - 1
A--------------AAUAAGCA-CAAAAGGAGGAAAUAUACAUUAACAGCUCUGUCAGCGACAAUUUCCGAUA--UGUGUUGCCUG------------AUUGUUGGUGAC-AUUUCCAU
.--------------........-........((((((...((((((((.....((((((((((..........--..))))).)))------------))))))))))..-)))))).. ( -20.90)
>consensus
AUUAACGAAUCAUCGAUUAAACA_GAGAUCGUAGA__AAUUCAUUACCGGAUUUGUCAACAACCAUUUCCGAUAAAUGAGUUAUCUGCGAAUGG___CGAUUGCCGCUGAC_GGCUUUCU
............................(((((((...(((((((..((((..((........))..))))...)))))))..)))))))...............(((....)))..... (-13.84 = -15.07 +   1.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:06 2006