Locus 4066

Sequence ID	3L_DroMel_CAF1
Location	11,850,576 – 11,850,668
Length	92
Max. P	0.946849

overview

Window 2

Location	11,850,576 – 11,850,668
Length	92
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	79.12
Mean single sequence MFE	-33.28
Consensus MFE	-20.05
Energy contribution	-20.50
Covariance contribution	0.45
Combinations/Pair	1.25
Mean z-score	-2.49
Structure conservation index	0.60
SVM decision value	1.37
SVM RNA-class probability	0.946849
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11850576 92 + 23771897
UGCACCA-AAGGCACCUGGACCUGGCCUGCAUU-CC--UUGUAUAUCGAGCAAAUGUCAGGCCGAAAGGUCAACGAACCCAGGUGAACACAGAAAG-
.......-....(((((((((((((((((((((-.(--(((.....))))..)))).))))))...))))........)))))))...........- ( -30.70)
>DroSec_CAF1 26596 90 + 1
UGCACCA-AAGGCACCUGGACCUGGCCUGCAUU-CC--UUGUAUACCAAGCAAAUGUCAGGCCGAAAGGUCAACGAACCUAGGUGAAC--AGAAAG-
..((((.-.(((......(((((((((((((((-.(--(((.....))))..)))).))))))...)))))......))).))))...--......- ( -31.20)
>DroEre_CAF1 25984 89 + 1
UGCACCA-GAGGCACCUGGUCCUGGCCCGCAUU-CC--UUGCAUGGCGAGCAAAUGUCAGGCCGAAAGGUCAACGCACCCAGGUGC-C--CGAAAG-
.......-(.(((((((((..((.(((.(((..-..--.)))..))).)).........((((....)))).......))))))))-)--).....- ( -37.60)
>DroYak_CAF1 27414 89 + 1
UGCACCA-GAGGCACCUGGACCUGGCCUGCAUU-CC--UUGUACGGCGAGCAAAUGUCAGGCCGAAAGGUCAACGAACCCAGGUGC-C--UGAAAG-
.......-.((((((((((..((.(((((((..-..--.)))).))).)).........((((....)))).......))))))))-)--).....- ( -40.00)
>DroAna_CAF1 26569 92 + 1
UGUAAAA-AAGGCACAUGGACCUGACUUGCAUU-GCUGUUGCAUGAAGAGCAAAUGUCAGGGCGAAAGGUCACCGAACCCAGGUGC-C--ACAAGCC
.......-..(((((.(((.((((((.....((-(((.((.....)).)))))..)))))).(....)..........))).))))-)--....... ( -30.20)
>DroPer_CAF1 25785 89 + 1
GGGGCCACGUGGCACAUGGACCUGGUCUGCACUGCC--GUGCAUGACAAGCAGGUGCCAAGAGGAAAGGUCACCGAACCCAGCUGA-----GGAGG-
((((((....)))...((((((((((((((((....--))))).)))...))))).)))...((........))...)))......-----.....- ( -30.00)
>consensus
UGCACCA_AAGGCACCUGGACCUGGCCUGCAUU_CC__UUGCAUGACGAGCAAAUGUCAGGCCGAAAGGUCAACGAACCCAGGUGA_C__AGAAAG_
............(((((((((((((((((((((......(((.......))))))).))))))...))))........)))))))............ (-20.05 = -20.50 +   0.45)

alignment

secondary structure

dotplot

Window 3

Location	11,850,576 – 11,850,668
Length	92
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	79.12
Mean single sequence MFE	-33.98
Consensus MFE	-18.66
Energy contribution	-20.69
Covariance contribution	2.03
Combinations/Pair	1.17
Mean z-score	-2.15
Structure conservation index	0.55
SVM decision value	0.67
SVM RNA-class probability	0.816291
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11850576 92 - 23771897
-CUUUCUGUGUUCACCUGGGUUCGUUGACCUUUCGGCCUGACAUUUGCUCGAUAUACAA--GG-AAUGCAGGCCAGGUCCAGGUGCCUU-UGGUGCA
-...........((((.((((.(.(.(((((...((((((.(((((.((.(.....).)--))-))))))))))))))).).).)))).-.)))).. ( -32.50)
>DroSec_CAF1 26596 90 - 1
-CUUUCU--GUUCACCUAGGUUCGUUGACCUUUCGGCCUGACAUUUGCUUGGUAUACAA--GG-AAUGCAGGCCAGGUCCAGGUGCCUU-UGGUGCA
-......--...((((.((((.(.(.(((((...((((((.(((((.((((.....)))--))-))))))))))))))).).).)))).-.)))).. ( -37.90)
>DroEre_CAF1 25984 89 - 1
-CUUUCG--G-GCACCUGGGUGCGUUGACCUUUCGGCCUGACAUUUGCUCGCCAUGCAA--GG-AAUGCGGGCCAGGACCAGGUGCCUC-UGGUGCA
-.....(--(-((((((((.......((....))((((((.(((((.((.((...)).)--))-))))))))))....)))))))))).-....... ( -36.60)
>DroYak_CAF1 27414 89 - 1
-CUUUCA--G-GCACCUGGGUUCGUUGACCUUUCGGCCUGACAUUUGCUCGCCGUACAA--GG-AAUGCAGGCCAGGUCCAGGUGCCUC-UGGUGCA
-......--.-(((((.((((.(.(.(((((...((((((.(((((.((.(.....).)--))-))))))))))))))).).).)))).-.))))). ( -37.00)
>DroAna_CAF1 26569 92 - 1
GGCUUGU--G-GCACCUGGGUUCGGUGACCUUUCGCCCUGACAUUUGCUCUUCAUGCAACAGC-AAUGCAAGUCAGGUCCAUGUGCCUU-UUUUACA
(((.(((--(-(.(((((.(((.(((((....)))))..)))((((((......(((....))-)..)))))))))))))))).)))..-....... ( -30.20)
>DroPer_CAF1 25785 89 - 1
-CCUCC-----UCAGCUGGGUUCGGUGACCUUUCCUCUUGGCACCUGCUUGUCAUGCAC--GGCAGUGCAGACCAGGUCCAUGUGCCACGUGGCCCC
-.....-----......(((...(....)....((.(.((((((..(((((((.(((((--....))))))).)))))....)))))).).))))). ( -29.70)
>consensus
_CUUUCU__G_GCACCUGGGUUCGUUGACCUUUCGGCCUGACAUUUGCUCGCCAUACAA__GG_AAUGCAGGCCAGGUCCAGGUGCCUC_UGGUGCA
............((((.(((..(.(.(((((...((((((.((((...................))))))))))))))).).)..)))...)))).. (-18.66 = -20.69 +   2.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:43 2006