Locus 1777

Sequence ID	2L_DroMel_CAF1
Location	4,858,735 – 4,858,889
Length	154
Max. P	0.908192

overview

Window 5

Location	4,858,735 – 4,858,837
Length	102
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	81.81
Mean single sequence MFE	-31.22
Consensus MFE	-22.84
Energy contribution	-23.45
Covariance contribution	0.61
Combinations/Pair	1.05
Mean z-score	-1.35
Structure conservation index	0.73
SVM decision value	0.07
SVM RNA-class probability	0.568526
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4858735 102 - 22407834
AAAUGUGCGCACUUUCGAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGCCGUUCGGUUCGUCGAGUCCUAGAUGAGCACUGUUCUGGUCUC--CGGCACAC
...((((((((((((...)))))))........(((.(((.((.((...((.....))(((((((........)))))))...)).)).))).)--))))))). ( -33.60)
>DroPse_CAF1 11968 100 - 1
AAAUGUGCGCACUUUUAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGCUGAU-GGUUGGUCGGGCCAUAGAUGGG---GGCCCUGGACUUCUCAGAAUAU
....(((((((((((...)))))))........((....)).)))).....((((.-((..(((((((((.........---)))))..))))))))))..... ( -30.40)
>DroEre_CAF1 9553 101 - 1
AAAUGUGCGCACUUUCAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGCUGAU-GGUUCGUCGAGUCCUAGAUGAGCACUGUUCUGGUCUC--UGGCACAC
...((((((((((((...)))))))............(((((((...((....)).-.)))))))(((.((.(((..........))))).)))--..))))). ( -32.90)
>DroYak_CAF1 9393 101 - 1
AAAUGUGCGCACUUUCAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGUUGAU-GGUUCGUCGAGUCCUAGAUGAGCACUGUUCUGGUCUC--CGGCACAC
...((((((((((((...)))))))........(((.(((.((.((.((....)).-.(((((((........)))))))...)).)).))).)--))))))). ( -32.60)
>DroAna_CAF1 13479 83 - 1
AAAUGUGCGCACUUUCAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGCUGAU-GGUUCGUCG------------------GUCUGCUCUC--CGGCACAG
...((((((((((((...)))))))...........((..(((((...(((.(((.-...))).))------------------)..)))))..--))))))). ( -29.70)
>DroPer_CAF1 11796 99 - 1
AGAUGUGCGCACUUUUAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGUUGAU-GGUUGGUCGGGCCAUAGAUGC----GGCUCUGGACUUCUCAGAAUAU
.((.(((((((((((...)))))))........((....)).)))).))......(-((..(((((((((........----)))))..))))..)))...... ( -28.10)
>consensus
AAAUGUGCGCACUUUCAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGCUGAU_GGUUCGUCGAGUCCUAGAUGAG___UGUUCUGGUCUC__CGGCACAC
...((((((((((((...)))))))...........((((((((...((....))...))))))))................................))))). (-22.84 = -23.45 +   0.61)

alignment

secondary structure

dotplot

Window 6

Location	4,858,764 – 4,858,865
Length	101
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	80.32
Mean single sequence MFE	-32.13
Consensus MFE	-23.41
Energy contribution	-23.22
Covariance contribution	-0.19
Combinations/Pair	1.14
Mean z-score	-2.12
Structure conservation index	0.73
SVM decision value	1.06
SVM RNA-class probability	0.908129
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4858764 101 + 22407834
U--AGGACUCGAC----GAACCGAACGGCGGAAGUGCUCGUCGCCAUUUUUAGUGCACUUCUCGAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUC----------GAACCGAA--
.--.((..((((.----...((((((((.((((((((.....).))))))).((((((((.....))))))))......))))))))((....))..))----------)).))...-- ( -28.50)
>DroVir_CAF1 9081 105 + 1
------UCCAGUC----GUGCC-AUCAGCGGAAGUGCUCGUCGCCAUUUUUAGUGCACUUCUUGAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGACUCGGCUCGGCCCGCCCAC-U--
------.((((((----(((((-(..(((((((((((.....))........((((((((.....))))))))..)))))))))))))))....)))).))...((....))...-.-- ( -35.50)
>DroGri_CAF1 9705 99 + 1
------UCUGGUCGGUGGGGCC-AUCAACGGAAGUGCUCGUCGCCAUUUUUAGUGCACUUCUCGAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUC----------GCCCAC-U--
------.......(((((((((-(..(((((((((((.....))........((((((((.....))))))))..)))))))))))))(((...)))..----------.)))))-)-- ( -35.20)
>DroWil_CAF1 13259 100 + 1
UUCAGGGCCUGCC----CAGCC-AUCAACGGAAGUGCUCGUCGCCAUUUUUAGUGCACUUCUUAAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUC----------GCCCA--C--
.((((((....))----).(((-(..(((((((((((.....))........((((((((.....))))))))..))))))))))))).....)))...----------.....--.-- ( -34.10)
>DroMoj_CAF1 8912 95 + 1
------UCUAGUU----GGGCC-AUCAACGGAAGUGCUCGUCGCCAUUUUUAGUGCACUUCUUGAAAGUGUGCACAUUUCCGUUUGGCAUCAAUGAUUC----------GCCCAC-U--
------....(((----(((((-(..(((((((((((.....))........((((((..((....)).))))))))))))))))))).))))).....----------......-.-- ( -29.20)
>DroAna_CAF1 13497 95 + 1
---------CGAC----GAACC-AUCAGCGGAAGUGCUCGUCGCCAUUUUUAGUGCACUUCUUGAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUC----------GGGCCAGACU
---------((((----((...-....((....))..)))))).........((((((((.....))))))))........(((((((.((........----------))))))))). ( -30.30)
>consensus
______UCUAGUC____GAGCC_AUCAACGGAAGUGCUCGUCGCCAUUUUUAGUGCACUUCUUGAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUC__________GCCCAC_U__
...................(((....(((((((((((.....))........((((((((.....))))))))..))))))))).)))............................... (-23.41 = -23.22 +  -0.19)

alignment

secondary structure

dotplot

Window 7

Location	4,858,764 – 4,858,865
Length	101
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	80.32
Mean single sequence MFE	-31.80
Consensus MFE	-21.06
Energy contribution	-21.00
Covariance contribution	-0.06
Combinations/Pair	1.05
Mean z-score	-1.65
Structure conservation index	0.66
SVM decision value	0.41
SVM RNA-class probability	0.726090
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4858764 101 - 22407834
--UUCGGUUC----------GAAUCAUUGAUGCCAAACGGAAAUGUGCGCACUUUCGAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGCCGUUCGGUUC----GUCGAGUCCU--A
--...(((((----------((.....(((.(((.(((((....(((((((((((...)))))))........((....)).)))).....))))).)))))----)))))).)).--. ( -32.40)
>DroVir_CAF1 9081 105 - 1
--A-GUGGGCGGGCCGAGCCGAGUCAUUGAUGCCAAACGGAAAUGUGCGCACUUUCAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGCUGAU-GGCAC----GACUGGA------
--.-...(((.(((...)))..))).(((.(((((..(((((..(((((((((((...)))))))........((....)).)))))))))....)-)))))----)).....------ ( -33.30)
>DroGri_CAF1 9705 99 - 1
--A-GUGGGC----------GAAUCAUUGAUGCCAAACGGAAAUGUGCGCACUUUCGAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGUUGAU-GGCCCCACCGACCAGA------
--.-((((((----------((....)))..(((((((((((..(((((((((((...)))))))........((....)).)))))))))))..)-))))))))........------ ( -34.40)
>DroWil_CAF1 13259 100 - 1
--G--UGGGC----------GAAUCAUUGAUGCCAAACGGAAAUGUGCGCACUUUUAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGUUGAU-GGCUG----GGCAGGCCCUGAA
--.--.((((----------...(((.....(((((((((((..(((((((((((...)))))))........((....)).)))))))))))..)-)))))----)....)))).... ( -34.90)
>DroMoj_CAF1 8912 95 - 1
--A-GUGGGC----------GAAUCAUUGAUGCCAAACGGAAAUGUGCACACUUUCAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGUUGAU-GGCCC----AACUAGA------
--(-((((((----------..(((((((....)))((((((..((((((...........))))))........((.....))..))))))))))-.))))----.)))...------ ( -28.70)
>DroAna_CAF1 13497 95 - 1
AGUCUGGCCC----------GAAUCAUUGAUGCCAAACGGAAAUGUGCGCACUUUCAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGCUGAU-GGUUC----GUCG---------
.........(----------((((((((...((.....((((..(((((((((((...)))))))........((....)).)))))))))).)))-)))))----)...--------- ( -27.10)
>consensus
__A_GUGGGC__________GAAUCAUUGAUGCCAAACGGAAAUGUGCGCACUUUCAAGAAGUGCACUAAAAAUGGCGACGAGCACUUCCGCUGAU_GGCUC____GACGAGA______
...............................(((...(((((..(((((((((((...)))))))........((....)).)))))))))......)))................... (-21.06 = -21.00 +  -0.06)

alignment

secondary structure

dotplot

Window 8

Location	4,858,797 – 4,858,889
Length	92
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	77.11
Mean single sequence MFE	-21.16
Consensus MFE	-15.80
Energy contribution	-15.80
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.75
SVM decision value	1.06
SVM RNA-class probability	0.908192
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4858797 92 + 22407834
GUCGCCAUUUUUAGUGCACUUCUCGAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUCGAACCGAA---------GC-CAUCAU-C--CCACCCACUUUACUG
...((........((((((((.....))))))))....(((.((((((.(((...))))))))).)))---------))-......-.--............... ( -18.00)
>DroPse_CAF1 12028 91 + 1
GUCGCCAUUUUUAGUGCACUUCUUAAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUCGGACUCGG----------U-UUUCCCCC--CCAUCC-CAUUUCUG
...((((......((((((((.....))))))))((......)).))))...........(((...((----------.-.......)--)..)))-........ ( -18.30)
>DroGri_CAF1 9737 94 + 1
GUCGCCAUUUUUAGUGCACUUCUCGAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUCGCCCAC-U---------GCCCACGGC-UCACCGUCCCCUUUUUUC
...(((.......((((((((.....))))))))........((..((((................-)---------))).)))))-.................. ( -19.99)
>DroWil_CAF1 13293 89 + 1
GUCGCCAUUUUUAGUGCACUUCUUAAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUCGCCCA--C---------GU-CCUGAC-U--UGG-CCACUCUUCCA
((.((((......((((((((.....)))))))).......(((..(((...........))).)--)---------).-......-.--)))-).))....... ( -22.00)
>DroAna_CAF1 13522 102 + 1
GUCGCCAUUUUUAGUGCACUUCUUGAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUCGGGCCAGACUAGACCAGGCUAGUCAC-U--CGUCCCUCUUUAUUG
...((((......((((((((.....))))))))((......)).))))..((((((...((((..((((((......))))))..-.--.))))....)))))) ( -29.90)
>DroPer_CAF1 11855 90 + 1
GUCGCCAUUUUUAGUGCACUUCUUAAAAGUGCGCACAUCUCCGUUUGGCAUCAAUGAUUCGGACUCGG----------U-UUUCCC-C--CCAUCC-CAUUUCUG
...((((......((((((((.....))))))))((......)).))))...........(((...((----------.-.....)-)--...)))-........ ( -18.80)
>consensus
GUCGCCAUUUUUAGUGCACUUCUUAAAAGUGCGCACAUUUCCGUUUGGCAUCAAUGAUUCGGACACGA_________GC_CAUCAC_C__CCAUCC_CUUUUCUG
...((((......((((((((.....))))))))((......)).))))........................................................ (-15.80 = -15.80 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:58 2006