Locus 1373

Sequence ID	X_DroMel_CAF1
Location	4,114,322 – 4,114,504
Length	182
Max. P	0.964056

overview

Window 8

Location	4,114,322 – 4,114,442
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.31
Mean single sequence MFE	-36.10
Consensus MFE	-31.24
Energy contribution	-31.11
Covariance contribution	-0.13
Combinations/Pair	1.07
Mean z-score	-2.72
Structure conservation index	0.87
SVM decision value	1.56
SVM RNA-class probability	0.964056
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4114322 120 + 22224390
GGCACAGCAUGAUUAUGGGCCAAAAGUUGGCUGGAUCACUUGGUGAGACACAGCAUCACCUUCAGCAUCAACAUCACCUGAAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGA
(((.((((.(((((...(((.....)))((((((.(((.(((((((......((..........)).(((........))).))))))).))).)))))).))))))))).)))...... ( -36.70)
>DroSec_CAF1 5532 120 + 1
UUCACAGCAUGAUUAUGGGCCAAAAAUUGGCUGGAUCACUUGGUGAGACACAGCAUCACCUGCAGCAUGAACACCACCUGAAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGA
.................((((((..(((((((((.(((.(((((((..((..(((.....)))....((.....))..))..))))))).))).))))).))))...))).)))...... ( -34.60)
>DroSim_CAF1 1025 120 + 1
GGCACAGCAUGAUUAUGGGCCAAAAAUUGGCUGGAUCACUUGGUGAGACACAGCAUCACCUGCAGCAUGAACACCACCUGAAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGA
(((.((((.(((((...(((((.....)))))((.(((.(((((((..((..(((.....)))....((.....))..))..))))))).))).)).....))))))))).)))...... ( -36.90)
>DroYak_CAF1 986 120 + 1
GGCACAGCAUGAUUCUGGGCCAAAAAUUGGCUGGAGCACUUGGUGAGCCACAGCAUCACCAUCAGCAUCAUCACCAUCUGAAUCACCAACUGAACCAGCUCAAUCAGUUGAGUCACUUGA
(((......(((((((((((((.....))))((..((...((((((((....)).))))))...))..))...)))...)))))).(((((((..........))))))).)))...... ( -36.20)
>consensus
GGCACAGCAUGAUUAUGGGCCAAAAAUUGGCUGGAUCACUUGGUGAGACACAGCAUCACCUGCAGCAUCAACACCACCUGAAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGA
.................((((((..(((((((((.(((.(((((((....(((........................)))..))))))).))).))))).))))...))).)))...... (-31.24 = -31.11 +  -0.13)

alignment

secondary structure

dotplot

Window 9

Location	4,114,362 – 4,114,482
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.61
Mean single sequence MFE	-25.00
Consensus MFE	-21.39
Energy contribution	-20.76
Covariance contribution	-0.63
Combinations/Pair	1.10
Mean z-score	-2.03
Structure conservation index	0.86
SVM decision value	0.89
SVM RNA-class probability	0.876200
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4114362 120 + 22224390
UGGUGAGACACAGCAUCACCUUCAGCAUCAACAUCACCUGAAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGAAUCAGUUCCAUCAGUUAAACCAAUUGAAUCAAUUGAGUCA
((((((......((..........)).(((........))).)))))).........((((((....))))))....(((.((((((...((((((.....))))))...)))))).))) ( -24.20)
>DroSec_CAF1 5572 120 + 1
UGGUGAGACACAGCAUCACCUGCAGCAUGAACACCACCUGAAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGAAUCAGUACCAUCAUUUAAGCCAAUUGAAUCAAUUGAGUAA
((((((..((..(((.....)))....((.....))..))..))))))(((((..((((((((....))))))....))..)))))............((((((((...)))))).)).. ( -24.80)
>DroSim_CAF1 1065 120 + 1
UGGUGAGACACAGCAUCACCUGCAGCAUGAACACCACCUGAAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGAAUCAGUACCAUCAUUUAAGCCAAUUGAAUCAAUUGAGUAA
((((((..((..(((.....)))....((.....))..))..))))))(((((..((((((((....))))))....))..)))))............((((((((...)))))).)).. ( -24.80)
>DroYak_CAF1 1026 120 + 1
UGGUGAGCCACAGCAUCACCAUCAGCAUCAUCACCAUCUGAAUCACCAACUGAACCAGCUCAAUCAGUUGAGUCACUUGAAUCAGUUCCAUCAAUUAAAUCAAUUGAAUCAAUUGAGUCA
((((((((....)).))))))((((.((.......))))))...(((((((((..........))))))).))....(((.((((((...((((((.....))))))...)))))).))) ( -26.20)
>consensus
UGGUGAGACACAGCAUCACCUGCAGCAUCAACACCACCUGAAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGAAUCAGUACCAUCAUUUAAACCAAUUGAAUCAAUUGAGUAA
((((((....(((........................)))..))))))(((((..((((((((....))))))....))..)))))............((((((((...)))))).)).. (-21.39 = -20.76 +  -0.63)

alignment

secondary structure

dotplot

Window 0

Location	4,114,402 – 4,114,504
Length	102
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-17.98
Consensus MFE	-14.98
Energy contribution	-15.22
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.69
Structure conservation index	0.83
SVM decision value	1.15
SVM RNA-class probability	0.923001
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4114402 102 + 22224390
AAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGAAUCAGUUCCAUCAGUUAAACCAAUUGAAUCAAUUGAGUCAGCUACACCAGCAUAUACAACAU
......(((((((..........))))))).......(((.((((((...((((((.....))))))...)))))).)))(((.....)))........... ( -18.50)
>DroSec_CAF1 5612 102 + 1
AAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGAAUCAGUACCAUCAUUUAAGCCAAUUGAAUCAAUUGAGUAAGCUACACCAGCAUUUACAACAU
.........(((....((((...((((((((..(((((((((.(......).))))))).....))..))))))))...))))....)))............ ( -17.60)
>DroSim_CAF1 1105 102 + 1
AAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGAAUCAGUACCAUCAUUUAAGCCAAUUGAAUCAAUUGAGUAAGCUACACCAGCAUUUACAACAU
.........(((....((((...((((((((..(((((((((.(......).))))))).....))..))))))))...))))....)))............ ( -17.60)
>DroYak_CAF1 1066 102 + 1
AAUCACCAACUGAACCAGCUCAAUCAGUUGAGUCACUUGAAUCAGUUCCAUCAAUUAAAUCAAUUGAAUCAAUUGAGUCAGCUACACCAACAUCUACACCAU
................((((...((((((((.(((.((((.(.((((.....)))).).)))).))).))))))))...))))................... ( -18.20)
>consensus
AAUCACCAACUGAACCAGCUCAAUCAGUUGAGCCACUUGAAUCAGUACCAUCAUUUAAACCAAUUGAAUCAAUUGAGUAAGCUACACCAGCAUUUACAACAU
.........(((....((((...((((((((..((.(((.....................))).))..))))))))...))))....)))............ (-14.98 = -15.22 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:43 2006