Locus 1774

Sequence ID	2L_DroMel_CAF1
Location	4,848,189 – 4,848,307
Length	118
Max. P	0.998330

overview

Window 8

Location	4,848,189 – 4,848,285
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	86.33
Mean single sequence MFE	-39.46
Consensus MFE	-33.30
Energy contribution	-34.34
Covariance contribution	1.04
Combinations/Pair	1.13
Mean z-score	-1.68
Structure conservation index	0.84
SVM decision value	0.61
SVM RNA-class probability	0.797808
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4848189 96 + 22407834
GAACAUGGGCUUUGGAGGCAAUUUUGGGCCUGGACCCGGACAAUGCGGUCCCCCCAUGGGGCCAAUGGGACCAGGAGGACCUCGCGGUCCCAUAAG
...((((((......((((........))))(((((((.....)).))))).))))))......((((((((..(((...)))..))))))))... ( -38.80)
>DroSec_CAF1 11588 96 + 1
GAACAUGGGCUUUGGAGGCAAUUUUGGGCCUGGUCCCGGACAAUGCGGUCCAUCCAUGGGGCCAAUGGGACCAGGAGGACCUUGCGGUCCCAUGGG
......(((((....((((........))))))))).((((......))))..((((((((((...(((.((....)).)))...)))))))))). ( -41.80)
>DroSim_CAF1 11678 96 + 1
GAACAUGGGCUUUGGAGGCAAUUUUGGGCCUGGUCCCGGACAAUGCGGUCCACCCAUGGGGCCAAUGGGACCAGGAGGACCUGGCGGUCCCAUGAG
...((((.(((.....))).........(((((((((((((......)))).((....))......))))))))).(((((....))))))))).. ( -42.40)
>DroEre_CAF1 11983 87 + 1
GAACAUGGGCUUUGGUGGUAAUUUCGGGCCUGGUCCCGGACCCUGCGGUCCA---------CCAAUGGGACCUGGAGGACCUUGUGGUCCCAUGAG
...((((((((.....(((..(((((((((((((...(((((....))))))---------))...))).))))))).)))....)).)))))).. ( -35.10)
>DroYak_CAF1 11821 87 + 1
GAACAUGGGCUUUGGGGGUAAUUUCGGGCCUGGUCCCGGUCCCUGUGGUCCA---------CCAAUGGGACCUGGAGGACCUUGUGGUCCCAUGAG
...(((((((((.(..(....)..))))))...(((.((((((..(((....---------)))..)))))).)))(((((....))))))))).. ( -39.20)
>consensus
GAACAUGGGCUUUGGAGGCAAUUUUGGGCCUGGUCCCGGACAAUGCGGUCCA_CCAUGGGGCCAAUGGGACCAGGAGGACCUUGCGGUCCCAUGAG
...((((((((...((((....(((...(((((((((((((......)))).((....))......))))))))).)))))))..)).)))))).. (-33.30 = -34.34 +   1.04)

alignment

secondary structure

dotplot

Window 9

Location	4,848,189 – 4,848,285
Length	96
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	86.33
Mean single sequence MFE	-37.66
Consensus MFE	-31.88
Energy contribution	-33.12
Covariance contribution	1.24
Combinations/Pair	1.04
Mean z-score	-2.84
Structure conservation index	0.85
SVM decision value	2.96
SVM RNA-class probability	0.997934
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4848189 96 - 22407834
CUUAUGGGACCGCGAGGUCCUCCUGGUCCCAUUGGCCCCAUGGGGGGACCGCAUUGUCCGGGUCCAGGCCCAAAAUUGCCUCCAAAGCCCAUGUUC
((.(((((((((.(((...))).))))))))).))...((((((.((((......))))((((....))))................))))))... ( -39.50)
>DroSec_CAF1 11588 96 - 1
CCCAUGGGACCGCAAGGUCCUCCUGGUCCCAUUGGCCCCAUGGAUGGACCGCAUUGUCCGGGACCAGGCCCAAAAUUGCCUCCAAAGCCCAUGUUC
..(((((((((....))))).(((((((((.....((....))..((((......))))))))))))).....................))))... ( -39.90)
>DroSim_CAF1 11678 96 - 1
CUCAUGGGACCGCCAGGUCCUCCUGGUCCCAUUGGCCCCAUGGGUGGACCGCAUUGUCCGGGACCAGGCCCAAAAUUGCCUCCAAAGCCCAUGUUC
..(((((((((....))))).(((((((((....((((...))))((((......))))))))))))).....................))))... ( -40.90)
>DroEre_CAF1 11983 87 - 1
CUCAUGGGACCACAAGGUCCUCCAGGUCCCAUUGG---------UGGACCGCAGGGUCCGGGACCAGGCCCGAAAUUACCACCAAAGCCCAUGUUC
..(((((((((....(((((.((((......))))---------.)))))....))))((((......))))................)))))... ( -34.20)
>DroYak_CAF1 11821 87 - 1
CUCAUGGGACCACAAGGUCCUCCAGGUCCCAUUGG---------UGGACCACAGGGACCGGGACCAGGCCCGAAAUUACCCCCAAAGCCCAUGUUC
..((((((.......((((((...((((((..(((---------....)))..)))))))))))).((.............))....))))))... ( -33.82)
>consensus
CUCAUGGGACCGCAAGGUCCUCCUGGUCCCAUUGGCCCCAUGG_UGGACCGCAUUGUCCGGGACCAGGCCCAAAAUUGCCUCCAAAGCCCAUGUUC
..(((((((((....))))).(((((((((....(((.....)))((((......))))))))))))).....................))))... (-31.88 = -33.12 +   1.24)

alignment

secondary structure

dotplot

Window 0

Location	4,848,217 – 4,848,307
Length	90
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	69.20
Mean single sequence MFE	-45.80
Consensus MFE	-25.43
Energy contribution	-26.30
Covariance contribution	0.87
Combinations/Pair	1.29
Mean z-score	-3.12
Structure conservation index	0.56
SVM decision value	3.07
SVM RNA-class probability	0.998330
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4848217 90 + 22407834
CCUGGACCCGGACAAUGCGGUCCC-CCCAUGGGGCCAAUGGGACCAGGA---GGACCUCGCGGUCCC----AUAA-GCAAU-AUGGGUCCCUGUGGUCCC--------------
(((((.(((((((......))))(-((....))).....))).))))).---(((((.((.((.(((----(((.-....)-))))).)).)).))))).-------------- ( -47.00)
>DroVir_CAF1 13401 113 + 1
CCCGGCCCUGGUCCUUGUGGACCCGGCCCUGGUCCCUGUG-GACCUGGCCCUGGUGCUUGCGGACCUGGCCCCGGCCCAAUGAUGCCGCCAAACUGCAAUAUGGGCGGCAAUAA
.((((.((.(((((....(.(((.((((..(((((....)-)))).))))..))).)....))))).))..))))........(((((((.............))))))).... ( -52.22)
>DroSec_CAF1 11616 90 + 1
CCUGGUCCCGGACAAUGCGGUCCA-UCCAUGGGGCCAAUGGGACCAGGA---GGACCUUGCGGUCCC----AUGG-GCAAU-AUGGGUCCCGGUGGUCAA--------------
(((((((((((......)(((((.-......)))))..)))))))))).---.(((((((.((.(((----(((.-....)-))))).))))).))))..-------------- ( -45.60)
>DroSim_CAF1 11706 90 + 1
CCUGGUCCCGGACAAUGCGGUCCA-CCCAUGGGGCCAAUGGGACCAGGA---GGACCUGGCGGUCCC----AUGA-GCAAU-AUGGGCCCCGGUGGUCCC--------------
(((((((((((((......)))).-((....))......))))))))).---((((((((.((.(((----(((.-....)-))))))))))..))))).-------------- ( -49.50)
>DroEre_CAF1 12011 81 + 1
CCUGGUCCCGGACCCUGCGGUCCA----------CCAAUGGGACCUGGA---GGACCUUGUGGUCCC----AUGA-GCAAU-AUGGGCCCCGGUGGCCCA--------------
((.(((((((((((....))))).----------.....)))))).)).---(((((....))))).----....-.....-.((((((.....))))))-------------- ( -39.60)
>DroYak_CAF1 11849 81 + 1
CCUGGUCCCGGUCCCUGUGGUCCA----------CCAAUGGGACCUGGA---GGACCUUGUGGUCCC----AUGA-GCAAU-AUGGGCCCCGGUGGUCCA--------------
.....(((.((((((..(((....----------)))..)))))).)))---((((((((.((.(((----(((.-....)-))))).))))).))))).-------------- ( -40.90)
>consensus
CCUGGUCCCGGACAAUGCGGUCCA__CCAUGGGGCCAAUGGGACCAGGA___GGACCUUGCGGUCCC____AUGA_GCAAU_AUGGGCCCCGGUGGUCCA______________
((.((((((((((......))))..((....))......)))))).))....(((((....)))))..................(((((.....)))))............... (-25.43 = -26.30 +   0.87)

alignment

secondary structure

dotplot

Window 1

Location	4,848,217 – 4,848,307
Length	90
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	69.20
Mean single sequence MFE	-44.97
Consensus MFE	-23.74
Energy contribution	-24.13
Covariance contribution	0.39
Combinations/Pair	1.23
Mean z-score	-2.77
Structure conservation index	0.53
SVM decision value	2.90
SVM RNA-class probability	0.997624
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4848217 90 - 22407834
--------------GGGACCACAGGGACCCAU-AUUGC-UUAU----GGGACCGCGAGGUCC---UCCUGGUCCCAUUGGCCCCAUGGG-GGGACCGCAUUGUCCGGGUCCAGG
--------------((((((.(.((..(((((-(....-.)))----))).))..).)))))---)(((((.(((.....(((....))-)((((......))))))).))))) ( -46.80)
>DroVir_CAF1 13401 113 - 1
UUAUUGCCGCCCAUAUUGCAGUUUGGCGGCAUCAUUGGGCCGGGGCCAGGUCCGCAAGCACCAGGGCCAGGUC-CACAGGGACCAGGGCCGGGUCCACAAGGACCAGGGCCGGG
....(((((((...((....))..)))))))....((((((..((((.(((.(....).)))..)))).))))-))......((..((((.(((((....)))))..)))).)) ( -56.50)
>DroSec_CAF1 11616 90 - 1
--------------UUGACCACCGGGACCCAU-AUUGC-CCAU----GGGACCGCAAGGUCC---UCCUGGUCCCAUUGGCCCCAUGGA-UGGACCGCAUUGUCCGGGACCAGG
--------------.........(((......-....)-))..----((((((....)))))---)(((((((((.....((....)).-.((((......))))))))))))) ( -40.40)
>DroSim_CAF1 11706 90 - 1
--------------GGGACCACCGGGGCCCAU-AUUGC-UCAU----GGGACCGCCAGGUCC---UCCUGGUCCCAUUGGCCCCAUGGG-UGGACCGCAUUGUCCGGGACCAGG
--------------((((((..(((..(((((-.....-..))----))).)))...)))))---)(((((((((....((((...)))-)((((......))))))))))))) ( -48.60)
>DroEre_CAF1 12011 81 - 1
--------------UGGGCCACCGGGGCCCAU-AUUGC-UCAU----GGGACCACAAGGUCC---UCCAGGUCCCAUUGG----------UGGACCGCAGGGUCCGGGACCAGG
--------------((((((.....)))))).-.....-....----((((((....)))))---)((.((((((.....----------.(((((....))))))))))).)) ( -39.90)
>DroYak_CAF1 11849 81 - 1
--------------UGGACCACCGGGGCCCAU-AUUGC-UCAU----GGGACCACAAGGUCC---UCCAGGUCCCAUUGG----------UGGACCACAGGGACCGGGACCAGG
--------------.(((((....((.(((((-.....-..))----))).))....)))))---(((.((((((..(((----------....)))..)))))).)))..... ( -37.60)
>consensus
______________UGGACCACCGGGGCCCAU_AUUGC_UCAU____GGGACCGCAAGGUCC___UCCAGGUCCCAUUGGCCCCAUGG__UGGACCGCAUGGUCCGGGACCAGG
...............((.((....)).))...................(((((....)))))....((.((((((...(....).......((((......)))))))))).)) (-23.74 = -24.13 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:51 2006