Locus 4643

Sequence ID	2R_DroMel_CAF1
Location	15,174,938 – 15,175,091
Length	153
Max. P	0.981987

overview

Window 4

Location	15,174,938 – 15,175,028
Length	90
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	82.84
Mean single sequence MFE	-34.52
Consensus MFE	-19.89
Energy contribution	-19.75
Covariance contribution	-0.14
Combinations/Pair	1.25
Mean z-score	-2.41
Structure conservation index	0.58
SVM decision value	0.05
SVM RNA-class probability	0.556608
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15174938 90 + 20766785
GCAAA--CUGGC---CACG-CCU-CGGGCCAAGAGUUGGUUUUGGCCAA--CUUUUGGCCAUUCCGC--ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG-
.....--(((((---...(-(..-..((((((((((((((....)))))--))))))))).....))--...((((((........)))))).)))))...- ( -39.00)
>DroSec_CAF1 5330 90 + 1
GCAAA--CUGGC---CACG-CCU-CGGGCCAAGAGUUGGUUUUGGCCAA--CUUUUGGCCAUUCCGC--ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG-
.....--(((((---...(-(..-..((((((((((((((....)))))--))))))))).....))--...((((((........)))))).)))))...- ( -39.00)
>DroSim_CAF1 5372 90 + 1
GCAAA--CUGGC---CACG-CCU-CGGGCCAAGAGUUGGUUUUGGCCAA--CUUUUGGCCAUUCCGC--ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG-
.....--(((((---...(-(..-..((((((((((((((....)))))--))))))))).....))--...((((((........)))))).)))))...- ( -39.00)
>DroEre_CAF1 5391 93 + 1
GCAAA--CUGGCCGCCACG-CCU-CGGGCCAUGAGUGGGUUUUGGCCAA--CUUUUGGCCAUUCCGC--ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG-
.....--(((((.(((.((-...-)))))..((.(((((...((((((.--....)))))).)))))--.))((((((........)))))).)))))...- ( -32.90)
>DroYak_CAF1 5350 91 + 1
GCAAA--CUGGC---CACG-CCUGUGGGCCAUGAGUUGGUUUUGGCCAA--CUUUUGGCCAUUCCGC--ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG-
.....--(((((---...(-(.....(((((.((((((((....)))))--))).))))).....))--...((((((........)))))).)))))...- ( -36.20)
>DroAna_CAF1 1486 96 + 1
GCAAAAGCAGUC---CACAACCU-CAUCCUAA--UCCUGUCCUGGCUAGGCCAUCUGACCGGUUGGUAUACGCGCGUGGCAUUUGGAAUGCAAGUCAGGUGU
......(((.((---((......-....((((--.((.(((.((((...))))...))).)))))).....((.....))...)))).)))........... ( -21.00)
>consensus
GCAAA__CUGGC___CACG_CCU_CGGGCCAAGAGUUGGUUUUGGCCAA__CUUUUGGCCAUUCCGC__ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG_
.......(((((.........................((...(((((((.....)))))))..)).......((((((........)))))).))))).... (-19.89 = -19.75 +  -0.14)

alignment

secondary structure

dotplot

Window 5

Location	15,174,958 – 15,175,051
Length	93
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	79.40
Mean single sequence MFE	-36.84
Consensus MFE	-21.50
Energy contribution	-21.45
Covariance contribution	-0.05
Combinations/Pair	1.30
Mean z-score	-3.27
Structure conservation index	0.58
SVM decision value	1.90
SVM RNA-class probability	0.981987
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15174958 93 + 20766785
GCCAAGAGUUGGUUUUGGCCAA--CUUUUGGCCAUUCCGC--ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG-----CUCUUUCACCUG------------GAAAGGGUUGA
(((((((((((((....)))))--))))))))((..((..--...((((((........))))))..(((((((-----......))))))------------)...))..)). ( -39.40)
>DroSec_CAF1 5350 93 + 1
GCCAAGAGUUGGUUUUGGCCAA--CUUUUGGCCAUUCCGC--ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG-----CUCUAUCACCUG------------GAAAGGGUUGA
(((((((((((((....)))))--))))))))((..((..--...((((((........))))))..(((((((-----......))))))------------)...))..)). ( -39.40)
>DroSim_CAF1 5392 93 + 1
GCCAAGAGUUGGUUUUGGCCAA--CUUUUGGCCAUUCCGC--ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG-----CUCUUUCACCUG------------GAAAGGGUUGA
(((((((((((((....)))))--))))))))((..((..--...((((((........))))))..(((((((-----......))))))------------)...))..)). ( -39.40)
>DroEre_CAF1 5414 93 + 1
GCCAUGAGUGGGUUUUGGCCAA--CUUUUGGCCAUUCCGC--ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG-----CUCUUUCACCUG------------GAAAGGGUUGC
(((.((((((((...((((((.--....)))))).)))))--...((((((........))))))..))))))(-----(((((((.....------------))))))))... ( -35.50)
>DroYak_CAF1 5371 93 + 1
GCCAUGAGUUGGUUUUGGCCAA--CUUUUGGCCAUUCCGC--ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG-----CUCUUUCACCUG------------GAAAGAGUUGA
((((.((((((((....)))))--))).))))....((..--((.((((((........)))))).))..)).(-----(((((((.....------------))))))))... ( -34.40)
>DroAna_CAF1 1509 112 + 1
CCUAA--UCCUGUCCUGGCUAGGCCAUCUGACCGGUUGGUAUACGCGCGUGGCAUUUGGAAUGCAAGUCAGGUGUGUGCCCCUGCCACAUGCCACCCAAAAUAGAAAUGGCAGC
.....--....(((.((((...))))...))).(((.((..(((((((.((((..(((.....))))))).)))))))..)).)))...(((((.............))))).. ( -32.92)
>consensus
GCCAAGAGUUGGUUUUGGCCAA__CUUUUGGCCAUUCCGC__ACACGCGUUAAAUUCCAAAUGCGAGUCAGGUG_____CUCUUUCACCUG____________GAAAGGGUUGA
(((.......((...(((((((.....)))))))..))....((.((((((........)))))).))..)))......(((((((.................))))))).... (-21.50 = -21.45 +  -0.05)

alignment

secondary structure

dotplot

Window 6

Location	15,174,958 – 15,175,051
Length	93
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.40
Mean single sequence MFE	-31.05
Consensus MFE	-18.33
Energy contribution	-18.88
Covariance contribution	0.56
Combinations/Pair	1.20
Mean z-score	-1.96
Structure conservation index	0.59
SVM decision value	0.58
SVM RNA-class probability	0.788192
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15174958 93 - 20766785
UCAACCCUUUC------------CAGGUGAAAGAG-----CACCUGACUCGCAUUUGGAAUUUAACGCGUGU--GCGGAAUGGCCAAAAG--UUGGCCAAAACCAACUCUUGGC
........(((------------((((((...(((-----(....).))).))))))))).....(((....--))).....(((((.((--((((......)))))).))))) ( -30.80)
>DroSec_CAF1 5350 93 - 1
UCAACCCUUUC------------CAGGUGAUAGAG-----CACCUGACUCGCAUUUGGAAUUUAACGCGUGU--GCGGAAUGGCCAAAAG--UUGGCCAAAACCAACUCUUGGC
........(((------------((((((...(((-----(....).))).))))))))).....(((....--))).....(((((.((--((((......)))))).))))) ( -30.80)
>DroSim_CAF1 5392 93 - 1
UCAACCCUUUC------------CAGGUGAAAGAG-----CACCUGACUCGCAUUUGGAAUUUAACGCGUGU--GCGGAAUGGCCAAAAG--UUGGCCAAAACCAACUCUUGGC
........(((------------((((((...(((-----(....).))).))))))))).....(((....--))).....(((((.((--((((......)))))).))))) ( -30.80)
>DroEre_CAF1 5414 93 - 1
GCAACCCUUUC------------CAGGUGAAAGAG-----CACCUGACUCGCAUUUGGAAUUUAACGCGUGU--GCGGAAUGGCCAAAAG--UUGGCCAAAACCCACUCAUGGC
((......(((------------((((((...(((-----(....).))).)))))))))......))(.((--(.((..((((((....--.))))))...))))).)..... ( -30.80)
>DroYak_CAF1 5371 93 - 1
UCAACUCUUUC------------CAGGUGAAAGAG-----CACCUGACUCGCAUUUGGAAUUUAACGCGUGU--GCGGAAUGGCCAAAAG--UUGGCCAAAACCAACUCAUGGC
........(((------------((((((...(((-----(....).))).))))))))).....(((....--))).....((((..((--((((......))))))..)))) ( -29.30)
>DroAna_CAF1 1509 112 - 1
GCUGCCAUUUCUAUUUUGGGUGGCAUGUGGCAGGGGCACACACCUGACUUGCAUUCCAAAUGCCACGCGCGUAUACCAACCGGUCAGAUGGCCUAGCCAGGACAGGA--UUAGG
....((..((((.(((((((((((((.(((((((........)))).........))).)))))))((.(((..(((....)))...)))))....)))))).))))--...)) ( -33.80)
>consensus
UCAACCCUUUC____________CAGGUGAAAGAG_____CACCUGACUCGCAUUUGGAAUUUAACGCGUGU__GCGGAAUGGCCAAAAG__UUGGCCAAAACCAACUCUUGGC
.......................((((((...........))))))........((((.......(((......)))...(((((((.....)))))))...))))........ (-18.33 = -18.88 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	15,174,991 – 15,175,091
Length	100
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	98.40
Mean single sequence MFE	-31.20
Consensus MFE	-29.80
Energy contribution	-29.84
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.16
Structure conservation index	0.96
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15174991 100 + 20766785
UCCGCACACGCGUUAAAUUCCAAAUGCGAGUCAGGUGCUCUUUCACCUGGAAAGGGUUGAGCAGCAGGCUGUUACCGGAUAGAAAGUUUUGCACGUGGUA
.((((((.((((((........)))))).))...((((.(((((.(((....)))....(((((....)))))........)))))....)))))))).. ( -31.70)
>DroSec_CAF1 5383 100 + 1
UCCGCACACGCGUUAAAUUCCAAAUGCGAGUCAGGUGCUCUAUCACCUGGAAAGGGUUGAGCAGCAGGCUGUUACCGGAUAGAAAGUUUUGCACGUGGUA
.((((((.((((((........)))))).))...((((((((((.(((....)))....(((((....)))))....)))))).......)))))))).. ( -31.31)
>DroSim_CAF1 5425 100 + 1
UCCGCACACGCGUUAAAUUCCAAAUGCGAGUCAGGUGCUCUUUCACCUGGAAAGGGUUGAGCAGCAGGCUGUUACCGGAUAGAAAGUUUUGCACGUGGUA
.((((((.((((((........)))))).))...((((.(((((.(((....)))....(((((....)))))........)))))....)))))))).. ( -31.70)
>DroEre_CAF1 5447 100 + 1
UCCGCACACGCGUUAAAUUCCAAAUGCGAGUCAGGUGCUCUUUCACCUGGAAAGGGUUGCCCAGCAGGCUGUUACCGGAUAGAAAGUUUUGCACGUGGUA
.((((((.((((((........)))))).))...((((.(((((..((((.((.((((((...))).))).)).))))...)))))....)))))))).. ( -31.10)
>DroYak_CAF1 5404 100 + 1
UCCGCACACGCGUUAAAUUCCAAAUGCGAGUCAGGUGCUCUUUCACCUGGAAAGAGUUGAGCAGCAGGCUGUUACCGGAUAGAAAGUUUUGCACGUGGUA
.((((((.((((((........)))))).))...((((.(((((..((((.((.((((........)))).)).))))...)))))....)))))))).. ( -30.20)
>consensus
UCCGCACACGCGUUAAAUUCCAAAUGCGAGUCAGGUGCUCUUUCACCUGGAAAGGGUUGAGCAGCAGGCUGUUACCGGAUAGAAAGUUUUGCACGUGGUA
.((((((.((((((........)))))).))...((((.(((((..((((.((.((((........)))).)).))))...)))))....)))))))).. (-29.80 = -29.84 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:34 2006