Locus 814

Sequence ID	2R_DroMel_CAF1
Location	3,845,542 – 3,845,675
Length	133
Max. P	0.942550

overview

Window 3

Location	3,845,542 – 3,845,644
Length	102
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	77.94
Mean single sequence MFE	-38.35
Consensus MFE	-25.66
Energy contribution	-26.05
Covariance contribution	0.39
Combinations/Pair	1.28
Mean z-score	-2.02
Structure conservation index	0.67
SVM decision value	1.33
SVM RNA-class probability	0.942550
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3845542 102 + 20766785
GGAUUGGGGGUCUG-GU---------CUGAGCUGCCUGGUCUGCUUCAUGGGGUGGAUUUUACGCCCCAGCCCUGGUUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUU
......(((((...-.(---------((.(((.(((((((..(((...(((((((.......))))))).....)))..)))))))))).))).)))))............. ( -39.40)
>DroSec_CAF1 101474 97 + 1
GGAUUGUGGGU---------------CUGGGCUGCCUGUUCUGCUUCAUGGGGUGGACUUUACGCCCCAGCCCUGGUUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUU
(((..(..(((---------------.......)))..)....((((((((((((.......)))))))(((((((....))))).)))))))...)))............. ( -32.10)
>DroSim_CAF1 118936 103 + 1
GGAUUGUGGGUCUGGGU---------CUGGGCUGCCAGGUCUGCUUCAUGGGGUGGAUUUUACGCCCCAGCCCUGGUUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUU
(((..(..(..((((((---------....))..))))..)..)(((((((((((.......)))))))(((((((....))))).))))))....)))............. ( -39.30)
>DroEre_CAF1 102767 109 + 1
GGGCUUG-G-UCUG-GUCUGGGCUGCCUGGGCUGCCUGGUCCGCUUCAUGGGGUGGAUUUUACGCCCCAGCCCUGGCUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUU
..(((((-(-(..(-(((.((((((...((((.....(((((((((....)))))))))....)))))))))).)))).))))))).....((....))............. ( -48.30)
>DroYak_CAF1 99748 92 + 1
GGGCUUG-GGUUUG-GCCUGGGUU------------------GCUUCAUGGGGUGGAUUUUACGCCCCAGCCCUGGUUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUC
(((((..-.....)-))))(((..------------------.((((((((((((.......)))))))(((((((....))))).)))))))...)))............. ( -36.50)
>DroAna_CAF1 97270 96 + 1
AGGUCCUGGACCUG-GA---------ACUUGCUGCUUGGC------CAAGGGGUGGAUUUAACGCCCCUGCCCUGGUUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUC
(((((...))))).-..---------(((((.((((..((------..(((((((.......)))))))(((.(((....))))))))..)((....))))))))))..... ( -34.50)
>consensus
GGAUUGGGGGUCUG_GU_________CUGGGCUGCCUGGUCUGCUUCAUGGGGUGGAUUUUACGCCCCAGCCCUGGUUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUU
((((.....))))........................((....((((((((((((.......)))))))(((((((....))))).)))))))....))............. (-25.66 = -26.05 +   0.39)

alignment

secondary structure

dotplot

Window 4

Location	3,845,542 – 3,845,644
Length	102
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	77.94
Mean single sequence MFE	-25.53
Consensus MFE	-18.04
Energy contribution	-17.93
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-1.26
Structure conservation index	0.71
SVM decision value	0.44
SVM RNA-class probability	0.735799
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3845542 102 - 20766785
AAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAACCAGGGCUGGGGCGUAAAAUCCACCCCAUGAAGCAGACCAGGCAGCUCAG---------AC-CAGACCCCCAAUCC
.............((....)).....(((((((....(((((.((((........)))).))).))......))))))).......---------..-.............. ( -24.70)
>DroSec_CAF1 101474 97 - 1
AAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAACCAGGGCUGGGGCGUAAAGUCCACCCCAUGAAGCAGAACAGGCAGCCCAG---------------ACCCACAAUCC
.............((..............(((....)))((((((((((.....))))...((.((........))))))))))..---------------..))....... ( -22.70)
>DroSim_CAF1 118936 103 - 1
AAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAACCAGGGCUGGGGCGUAAAAUCCACCCCAUGAAGCAGACCUGGCAGCCCAG---------ACCCAGACCCACAAUCC
.............(((.............(((....)))((((((((((...................))....((((....))))---------.))))).)))....))) ( -24.31)
>DroEre_CAF1 102767 109 - 1
AAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAGCCAGGGCUGGGGCGUAAAAUCCACCCCAUGAAGCGGACCAGGCAGCCCAGGCAGCCCAGAC-CAGA-C-CAAGCCC
.............((...........(((((((..(((((((.((((........)))).))).))..))..))))))).((....))........)-)...-.-....... ( -32.00)
>DroYak_CAF1 99748 92 - 1
GAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAACCAGGGCUGGGGCGUAAAAUCCACCCCAUGAAGC------------------AACCCAGGC-CAAACC-CAAGCCC
.............((............(((((....)))))(((((((.(.......).))))....)))------------------...)).(((-......-...))). ( -21.50)
>DroAna_CAF1 97270 96 - 1
GAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAACCAGGGCAGGGGCGUUAAAUCCACCCCUUG------GCCAAGCAGCAAGU---------UC-CAGGUCCAGGACCU
.............((((((.........((((....))))((((((((.(.......).)))))..------)))........)))---------))-)(((((...))))) ( -28.00)
>consensus
AAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAACCAGGGCUGGGGCGUAAAAUCCACCCCAUGAAGCAGACCAGGCAGCCCAG_________AC_CAGACCCACAACCC
.............((....))(((...(((((....)))))..(((((.(.......).))))))))............................................. (-18.04 = -17.93 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	3,845,564 – 3,845,675
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.05
Mean single sequence MFE	-36.03
Consensus MFE	-21.07
Energy contribution	-21.10
Covariance contribution	0.03
Combinations/Pair	1.16
Mean z-score	-2.10
Structure conservation index	0.58
SVM decision value	1.24
SVM RNA-class probability	0.934363
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3845564 111 + 20766785
UGCCUGGUCUGCUUCAUGGGGUGGAUUUUACGCCCCAGCCCUGGUUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUUUACGGUAUU--UGUUGGCUCAAGCAUUUUACGG-------
.(((((((..(((...(((((((.......))))))).....)))..)))))))((..(.((((.(((((..........))))).)))--).)..))...............------- ( -43.90)
>DroPse_CAF1 94662 103 + 1
----GGGC------UCUGGGGUUGAUUUAACGCCCCGUCCCUGGUCUACCAGGCGUCGAGGAAUUCCGAAAAAGUGUUUUUACGGUAUUUCUGUUGGCACAAGUAUUUUUCCG-------
----((((------((.(((((.........)))))(.((((((....))))).).)))).............(((((...((((.....)))).))))).........))).------- ( -30.20)
>DroWil_CAF1 156340 113 + 1
GGCAAAAGCUUUUUUUUGGGGUUGAUUUUACGCCCCGUCCCUGGCUUACCAGGCGUUGAGAAAUUCCGUA-AAGUGUUUUUACGGUAUU--UUU-G---CCAGUGUUAUACGACGACGAC
((((((((...(((((((((((.........)))))...(((((....)))))....))))))..(((((-(((...))))))))..))--)))-)---)).(((((....))).))... ( -32.10)
>DroYak_CAF1 99770 101 + 1
----------GCUUCAUGGGGUGGAUUUUACGCCCCAGCCCUGGUUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUCUACGGUAUU--UGUUGGCUCAAGCAUUUUACGG-------
----------((((..(((((((.......)))))))(((.(((....))))))((..(.((((.(((((..........))))).)))--).)..))..)))).........------- ( -37.10)
>DroAna_CAF1 97292 105 + 1
UGCUUGGC------CAAGGGGUGGAUUUAACGCCCCUGCCCUGGUUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUCUACGGUAUU--UGUUGGCUCAAGCAUUUUCCGG-------
((((((((------(.(((((((.......)))))))(((((((....))))).)).((.((((.(((((..........))))).)))--).))))).))))))........------- ( -42.70)
>DroPer_CAF1 95580 103 + 1
----GGGC------UCUGGGGUUGAUUUAACGCCCCGUCCCUGGUCUACCAGGCGUCGAGGAAUUCCGAAAAAGUGUUUUUACGGUAUUUCUGUUGGCACAAGUAUUUUUCCG-------
----((((------((.(((((.........)))))(.((((((....))))).).)))).............(((((...((((.....)))).))))).........))).------- ( -30.20)
>consensus
____GGGC______CAUGGGGUGGAUUUAACGCCCCGGCCCUGGUUUACCAGGCGUUGAGGAAUUCCGUAUAAGUGUUUUUACGGUAUU__UGUUGGCUCAAGCAUUUUACGG_______
................((((((.........))))))..(((((....))))).(((((.((((.(((((..........))))).)))..).)))))...................... (-21.07 = -21.10 +   0.03)

alignment

secondary structure

dotplot

Window 6

Location	3,845,564 – 3,845,675
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.05
Mean single sequence MFE	-28.57
Consensus MFE	-18.25
Energy contribution	-18.58
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	0.64
SVM decision value	1.25
SVM RNA-class probability	0.935598
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3845564 111 - 20766785
-------CCGUAAAAUGCUUGAGCCAACA--AAUACCGUAAAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAACCAGGGCUGGGGCGUAAAAUCCACCCCAUGAAGCAGACCAGGCA
-------........((((((((((....--....(((((.((....)).))))).............((((....))))))))((((.(.......).))))...........)))))) ( -30.80)
>DroPse_CAF1 94662 103 - 1
-------CGGAAAAAUACUUGUGCCAACAGAAAUACCGUAAAAACACUUUUUCGGAAUUCCUCGACGCCUGGUAGACCAGGGACGGGGCGUUAAAUCAACCCCAGA------GCCC----
-------.((((......((((....)))).....(((.((((....)))).)))..)))).((.(.(((((....)))))).))(((.(((.....))))))...------....---- ( -24.20)
>DroWil_CAF1 156340 113 - 1
GUCGUCGUCGUAUAACACUGG---C-AAA--AAUACCGUAAAAACACUU-UACGGAAUUUCUCAACGCCUGGUAAGCCAGGGACGGGGCGUAAAAUCAACCCCAAAAAAAAGCUUUUGCC
...................((---(-(((--(...(((((((.....))-)))))............(((((....)))))...((((...........))))..........))))))) ( -29.70)
>DroYak_CAF1 99770 101 - 1
-------CCGUAAAAUGCUUGAGCCAACA--AAUACCGUAGAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAACCAGGGCUGGGGCGUAAAAUCCACCCCAUGAAGC----------
-------.........((((.((((....--....(((((..........))))).............((((....))))))))((((.(.......).))))...))))---------- ( -26.80)
>DroAna_CAF1 97292 105 - 1
-------CCGGAAAAUGCUUGAGCCAACA--AAUACCGUAGAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAACCAGGGCAGGGGCGUUAAAUCCACCCCUUG------GCCAAGCA
-------........((((((.((((...--....(((((..........)))))...........((((((....))).)))(((((.(.......).)))))))------)))))))) ( -35.70)
>DroPer_CAF1 95580 103 - 1
-------CGGAAAAAUACUUGUGCCAACAGAAAUACCGUAAAAACACUUUUUCGGAAUUCCUCGACGCCUGGUAGACCAGGGACGGGGCGUUAAAUCAACCCCAGA------GCCC----
-------.((((......((((....)))).....(((.((((....)))).)))..)))).((.(.(((((....)))))).))(((.(((.....))))))...------....---- ( -24.20)
>consensus
_______CCGUAAAAUACUUGAGCCAACA__AAUACCGUAAAAACACUUAUACGGAAUUCCUCAACGCCUGGUAAACCAGGGACGGGGCGUAAAAUCAACCCCAUA______GCCA____
...................................(((((.((....)).)))))............(((((....)))))...((((...........))))................. (-18.25 = -18.58 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:06 2006