Locus 7634

Sequence ID	2L_DroMel_CAF1
Location	21,213,744 – 21,213,880
Length	136
Max. P	0.993882

overview

Window 9

Location	21,213,744 – 21,213,840
Length	96
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	77.40
Mean single sequence MFE	-31.48
Consensus MFE	-15.50
Energy contribution	-16.17
Covariance contribution	0.67
Combinations/Pair	1.24
Mean z-score	-1.94
Structure conservation index	0.49
SVM decision value	0.19
SVM RNA-class probability	0.626638
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21213744 96 + 22407834
AUC---CGA---GGCCAGCGAGGCGGAGGAGGAGGCACGUAAUAAGAAGAAAAAAAAGUGUCCUGGCAAGGAUGGCUGGUCUUCCGAUUCAGAAGAACAGCC
(((---(..---.(((((.((.((.................................)).)))))))..))))(((((.(((((.......))))).))))) ( -29.71)
>DroVir_CAF1 4393 99 + 1
GUCCUUUGAGUCGGCCAGCGAGGCCGAAG---AGACCAAAAAGAAGAUCAAGAAAAAAUGCCCCGGCAAGGAUGGCUGGUCCUCGGACUCCGAGGAGCAGGC
(((((((((.((((((.....))))))..---...............)))).......(((....))))))))(.(((.(((((((...))))))).))).) ( -36.87)
>DroGri_CAF1 4765 99 + 1
GUCCUUUGAGUCAGCCAGCGAAGCGGAAG---AGGCCAAAAAGAAGAUCAAGAAGAAAUGUCCAGGCAAAGAUGGCUGGUCCUCAGACUCUGAGGAACAGGC
.(((((.(((((.((.......))(((..---.(((((.........((.....))..(((....)))....)))))..)))...))))).)))))...... ( -28.10)
>DroEre_CAF1 3742 96 + 1
GUC---GGA---GGCCAGCGAGGCGGAGGAGGAGACCCGUAAUAAGAAGAAAAAGAAGUGUCCUGGUAAGGAUGGCUGGUCCUCCGAUUCAGAAGAGCAGCC
(((---(((---(((((((...((((....(....)))))...................(((((....))))).))))).)))))))).............. ( -34.90)
>DroYak_CAF1 3655 96 + 1
AUC---UGA---GGCUAGCGAGGCGGAGGAGGAGGCCCGUAAUAAGAAGAAAAAAAAGUGUCCUGGCAAGGAUGGCUGGUCCUCCGAUUCAGAGGAACAGCC
.((---(((---((((.....)))((((((...(((((.......).............(((((....)))))))))..))))))..))))))......... ( -29.30)
>DroAna_CAF1 3873 96 + 1
GUC---CGA---GGCCAGUGAAGCCGAGGAGGAGGCUCGCAGUAAGAAGAAGAAGAAGUGUCCCGGAAAGGACGGUUGGUCGUCCGACUCCGAGGAGCAACC
.((---(..---(((.......)))..)))((..(((((((.(.............).)))..((((..((((((....))))))...))))..))))..)) ( -30.02)
>consensus
GUC___UGA___GGCCAGCGAGGCGGAGGAGGAGGCCCGUAAUAAGAAGAAAAAAAAGUGUCCUGGCAAGGAUGGCUGGUCCUCCGACUCAGAGGAACAGCC
.............(((.....)))...................................((((......))))(((((.(((((.......))))).))))) (-15.50 = -16.17 +   0.67)

alignment

secondary structure

dotplot

Window 0

Location	21,213,744 – 21,213,840
Length	96
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	77.40
Mean single sequence MFE	-29.56
Consensus MFE	-19.92
Energy contribution	-19.37
Covariance contribution	-0.55
Combinations/Pair	1.47
Mean z-score	-2.52
Structure conservation index	0.67
SVM decision value	1.92
SVM RNA-class probability	0.982617
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21213744 96 - 22407834
GGCUGUUCUUCUGAAUCGGAAGACCAGCCAUCCUUGCCAGGACACUUUUUUUUCUUCUUAUUACGUGCCUCCUCCUCCGCCUCGCUGGCC---UCG---GAU
(((((.(((((((...))))))).)))))((((.....(((.(((...................))))))........(((.....))).---..)---))) ( -28.21)
>DroVir_CAF1 4393 99 - 1
GCCUGCUCCUCGGAGUCCGAGGACCAGCCAUCCUUGCCGGGGCAUUUUUUCUUGAUCUUCUUUUUGGUCU---CUUCGGCCUCGCUGGCCGACUCAAAGGAC
(.(((.(((((((...))))))).))).).(((((...(((............((((........)))).---..((((((.....))))))))).))))). ( -36.40)
>DroGri_CAF1 4765 99 - 1
GCCUGUUCCUCAGAGUCUGAGGACCAGCCAUCUUUGCCUGGACAUUUCUUCUUGAUCUUCUUUUUGGCCU---CUUCCGCUUCGCUGGCUGACUCAAAGGAC
......((((..(((((.(((((((((.((....)).)))).((........)).))))).....((((.---.............)))))))))..)))). ( -26.34)
>DroEre_CAF1 3742 96 - 1
GGCUGCUCUUCUGAAUCGGAGGACCAGCCAUCCUUACCAGGACACUUCUUUUUCUUCUUAUUACGGGUCUCCUCCUCCGCCUCGCUGGCC---UCC---GAC
...............(((((((.(((((..((((....)))).....................((((........))))....)))))))---)))---)). ( -28.60)
>DroYak_CAF1 3655 96 - 1
GGCUGUUCCUCUGAAUCGGAGGACCAGCCAUCCUUGCCAGGACACUUUUUUUUCUUCUUAUUACGGGCCUCCUCCUCCGCCUCGCUAGCC---UCA---GAU
(((((.(((((((...))))))).))))).((((....))))..........(((........(((((..........))).))......---..)---)). ( -26.19)
>DroAna_CAF1 3873 96 - 1
GGUUGCUCCUCGGAGUCGGACGACCAACCGUCCUUUCCGGGACACUUCUUCUUCUUCUUACUGCGAGCCUCCUCCUCGGCUUCACUGGCC---UCG---GAC
((..(((((((((((..(((((......))))).)))))))...............(.....).))))..))(((..((((.....))))---..)---)). ( -31.60)
>consensus
GGCUGCUCCUCUGAAUCGGAGGACCAGCCAUCCUUGCCAGGACACUUCUUCUUCUUCUUAUUACGGGCCUCCUCCUCCGCCUCGCUGGCC___UCA___GAC
(((((.(((((((...))))))).))))).((((....))))....................................(((.....)))............. (-19.92 = -19.37 +  -0.55)

alignment

secondary structure

dotplot

Window 1

Location	21,213,778 – 21,213,880
Length	102
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	84.44
Mean single sequence MFE	-29.82
Consensus MFE	-19.22
Energy contribution	-19.42
Covariance contribution	0.20
Combinations/Pair	1.21
Mean z-score	-3.14
Structure conservation index	0.64
SVM decision value	1.67
SVM RNA-class probability	0.970925
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21213778 102 + 22407834
AAUAAGAAG------------AAAAAAAAGUGUCCUGGCAAGGAUGG---CUGGUCUUCCGAUUCAGAAGAACAGCCAGAAAGUGAGGAGGAGGAGGAGGAGCCACCGCACUAUGAA
.........------------.......((((((((.((.....(((---(((.(((((.......))))).))))))....)).))))...((.((.....)).)).))))..... ( -30.40)
>DroSec_CAF1 3737 102 + 1
AAUAAGAAG------------AAAAAAAAGUGUCCUGGCAAGGAUGG---CUGGUCUUCUGAUUCAGAAGAACAGCCGGAAAGCGAGGAGGAAGAGGAGGAGCCACCGCACUAUGAA
.........------------.......((((((((.((.....(((---(((.(((((((...))))))).))))))....)).))))......((.(....).)).))))..... ( -32.90)
>DroEre_CAF1 3776 102 + 1
AAUAAGAAG------------AAAAAGAAGUGUCCUGGUAAGGAUGG---CUGGUCCUCCGAUUCAGAAGAGCAGCCAGAGAGCGAGGAGGAAGAGGAGGAACCACCGCACUAUGAA
.........------------.......((((((((....)))..((---.(((((((((..(((......((.........))......)))..))))).)))))))))))..... ( -29.30)
>DroWil_CAF1 4314 117 + 1
AAUCAGAUGAAAAAGAAGGCGAAAAAGAAAUGUCCUGGCAAAGAUGGAACCUGGUCAUCAGACUCCGAAGAGCAAGCUGAGAGUGAGGAGGAAGAAGAGGAGCCACCUCAUUAUGAA
..(((........((...((..........(((....)))....((((..(((.....)))..))))....))...))...(((((((.((...........)).))))))).))). ( -21.80)
>DroYak_CAF1 3689 102 + 1
AAUAAGAAG------------AAAAAAAAGUGUCCUGGCAAGGAUGG---CUGGUCCUCCGAUUCAGAGGAACAGCCAGAGAGCGAGGAGGAAGAGGAGGAGCCACCUCACUAUGAA
.........------------.......(((.((((.((.....(((---(((.(((((.......))))).))))))....)).))))....((((.(....).)))))))..... ( -34.70)
>consensus
AAUAAGAAG____________AAAAAAAAGUGUCCUGGCAAGGAUGG___CUGGUCCUCCGAUUCAGAAGAACAGCCAGAGAGCGAGGAGGAAGAGGAGGAGCCACCGCACUAUGAA
............................((((((((.((.....(((...(((.(((((.......))))).))))))....)).))))......((.(....).)).))))..... (-19.22 = -19.42 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	21,213,778 – 21,213,880
Length	102
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	84.44
Mean single sequence MFE	-28.17
Consensus MFE	-18.08
Energy contribution	-17.40
Covariance contribution	-0.68
Combinations/Pair	1.29
Mean z-score	-4.07
Structure conservation index	0.64
SVM decision value	2.43
SVM RNA-class probability	0.993882
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21213778 102 - 22407834
UUCAUAGUGCGGUGGCUCCUCCUCCUCCUCCUCACUUUCUGGCUGUUCUUCUGAAUCGGAAGACCAG---CCAUCCUUGCCAGGACACUUUUUUUU------------CUUCUUAUU
.....((((.((.((...........)).)).))))...((((((.(((((((...))))))).)))---)))((((....))))...........------------......... ( -27.30)
>DroSec_CAF1 3737 102 - 1
UUCAUAGUGCGGUGGCUCCUCCUCUUCCUCCUCGCUUUCCGGCUGUUCUUCUGAAUCAGAAGACCAG---CCAUCCUUGCCAGGACACUUUUUUUU------------CUUCUUAUU
.....((((.((.(....).))......((((.((.....(((((.(((((((...))))))).)))---))......)).)))))))).......------------......... ( -28.80)
>DroEre_CAF1 3776 102 - 1
UUCAUAGUGCGGUGGUUCCUCCUCUUCCUCCUCGCUCUCUGGCUGCUCUUCUGAAUCGGAGGACCAG---CCAUCCUUACCAGGACACUUCUUUUU------------CUUCUUAUU
.....((((.((.((...........)).)).))))...((((((.(((((((...))))))).)))---)))((((....))))...........------------......... ( -27.60)
>DroWil_CAF1 4314 117 - 1
UUCAUAAUGAGGUGGCUCCUCUUCUUCCUCCUCACUCUCAGCUUGCUCUUCGGAGUCUGAUGACCAGGUUCCAUCUUUGCCAGGACAUUUCUUUUUCGCCUUCUUUUUCAUCUGAUU
........((((((((..........(((..(((...((((...((((....)))))))))))..)))..........)))((((....))))....)))))............... ( -23.35)
>DroYak_CAF1 3689 102 - 1
UUCAUAGUGAGGUGGCUCCUCCUCUUCCUCCUCGCUCUCUGGCUGUUCCUCUGAAUCGGAGGACCAG---CCAUCCUUGCCAGGACACUUUUUUUU------------CUUCUUAUU
.....(((((((.((...........)).)))))))...((((((.(((((((...))))))).)))---)))((((....))))...........------------......... ( -33.80)
>consensus
UUCAUAGUGCGGUGGCUCCUCCUCUUCCUCCUCGCUCUCUGGCUGUUCUUCUGAAUCGGAAGACCAG___CCAUCCUUGCCAGGACACUUUUUUUU____________CUUCUUAUU
.....((((.((.((...........)).)).))))....(((((.(((((((...))))))).)))...)).((((....))))................................ (-18.08 = -17.40 +  -0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:36 2006