Locus 8894

Sequence ID	3R_DroMel_CAF1
Location	23,858,227 – 23,858,347
Length	120
Max. P	0.978694

overview

Window 1

Location	23,858,227 – 23,858,321
Length	94
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	76.51
Mean single sequence MFE	-32.14
Consensus MFE	-15.44
Energy contribution	-17.02
Covariance contribution	1.58
Combinations/Pair	1.14
Mean z-score	-2.49
Structure conservation index	0.48
SVM decision value	1.48
SVM RNA-class probability	0.957543
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23858227 94 + 27905053
AGGACAAGCAGAUAGUGUCUGCUGUCCG----UUCGGCUCCUGAGUUGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCAAUUCUUGGCCGUGUC
.(((((.((((((...))))))))))).----...(((.(..((((((..(((((....)))))..)))))).......((((.....)))).).))) ( -35.70)
>DroSec_CAF1 63765 94 + 1
AGGACAAGCAGAUAGUGUCUGCUGUCCG----UUCGGCUCCUGAGCUGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCAAUUCUUGGUCGUGUC
.(((((.((((((...))))))))))).----...(((....((((((..(((((....)))))..)))))).......)))................ ( -37.20)
>DroSim_CAF1 63209 94 + 1
AGGACAAGCAGAUAUUGUCUGCUGUCCG----UUCGGCUCCUGAGCUGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCAAUUCUUGGCCGUGUC
.(((((.((((((...))))))))))).----...(((.(..((((((..(((((....)))))..)))))).......((((.....)))).).))) ( -38.10)
>DroEre_CAF1 67780 82 + 1
AGGACAAGG----AGUGUUUGCUGUCCG----UUCGGCUCCU--------GAGCUCCACAGCUCCACGGCUCCUUCCUUUCCAAUUCUUGGCCGUGUC
((((..(((----(((((..(((((..(----(((((...))--------))))...)))))...)).))))))))))..(((.....)))....... ( -24.20)
>DroYak_CAF1 65727 90 + 1
AGGACAAGCAGAUAGUGUCUGCUGUCCGUCCAUUCGGCUACU--------GAGCUUCUCAGCUCCACAGCUCCUUCCUUUCCAAUGCUUGGCCGUGUC
.(((((.((((((...))))))))))).......((((((..--------(((((....)))))...(((...............))))))))).... ( -29.66)
>DroAna_CAF1 65429 79 + 1
AGGACAAGCAGAUAGCGGAUAGUGUCUG----UUCACUUAUCCUGCUGCUG-GCUUCCCGUCGGCCCUGCUC--------------CUUGGCCGUGUC
.((.(((((((..(((((((((((....----..))).))))).)))((((-((.....)))))).))))).--------------..)).))..... ( -28.00)
>consensus
AGGACAAGCAGAUAGUGUCUGCUGUCCG____UUCGGCUCCUGAGCUGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCAAUUCUUGGCCGUGUC
.(((((.(((((.....)))))))))).......................(((((....)))))(((.(((..................))).))).. (-15.44 = -17.02 +   1.58)

alignment

secondary structure

dotplot

Window 2

Location	23,858,227 – 23,858,321
Length	94
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	76.51
Mean single sequence MFE	-33.63
Consensus MFE	-17.22
Energy contribution	-19.58
Covariance contribution	2.36
Combinations/Pair	1.08
Mean z-score	-2.59
Structure conservation index	0.51
SVM decision value	1.82
SVM RNA-class probability	0.978694
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23858227 94 - 27905053
GACACGGCCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAACUCAGGAGCCGAA----CGGACAGCAGACACUAUCUGCUUGUCCU
......((((.....))))..((...(((.(((.(((((....))))).))).))).....))...----.((((((((((.....))))).))))). ( -36.10)
>DroSec_CAF1 63765 94 - 1
GACACGACCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAGCUCAGGAGCCGAA----CGGACAGCAGACACUAUCUGCUUGUCCU
..............(((((.......(((((((.(((((....))))).)))))))....))))).----.((((((((((.....))))).))))). ( -40.40)
>DroSim_CAF1 63209 94 - 1
GACACGGCCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAGCUCAGGAGCCGAA----CGGACAGCAGACAAUAUCUGCUUGUCCU
......((((.....))))..((...(((((((.(((((....))))).))))))).....))...----.((((((((((.....))))).))))). ( -42.70)
>DroEre_CAF1 67780 82 - 1
GACACGGCCAAGAAUUGGAAAGGAAGGAGCCGUGGAGCUGUGGAGCUC--------AGGAGCCGAA----CGGACAGCAAACACU----CCUUGUCCU
..(((((((.....((....))....).))))))(((((....)))))--------..........----.((((((........----..)))))). ( -23.80)
>DroYak_CAF1 65727 90 - 1
GACACGGCCAAGCAUUGGAAAGGAAGGAGCUGUGGAGCUGAGAAGCUC--------AGUAGCCGAAUGGACGGACAGCAGACACUAUCUGCUUGUCCU
..(((((((.....((....))....).))))))(((((....)))))--------....(((....)).)((((((((((.....))))).))))). ( -31.10)
>DroAna_CAF1 65429 79 - 1
GACACGGCCAAG--------------GAGCAGGGCCGACGGGAAGC-CAGCAGCAGGAUAAGUGAA----CAGACACUAUCCGCUAUCUGCUUGUCCU
(((((((((...--------------......)))))..((....)-)(((((..(((((.(((..----....)))))))).....))))))))).. ( -27.70)
>consensus
GACACGGCCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAGCUCAGGAGCCGAA____CGGACAGCAGACACUAUCUGCUUGUCCU
..(((((((.....((....))....).))))))(((((....))))).......................((((((((((.....))))).))))). (-17.22 = -19.58 +   2.36)

alignment

secondary structure

dotplot

Window 3

Location	23,858,255 – 23,858,347
Length	92
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	90.11
Mean single sequence MFE	-23.77
Consensus MFE	-16.66
Energy contribution	-19.30
Covariance contribution	2.64
Combinations/Pair	1.08
Mean z-score	-2.06
Structure conservation index	0.70
SVM decision value	0.10
SVM RNA-class probability	0.585525
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23858255 92 + 27905053
--UUCGGCUCCUGAGUUGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCAAUUCUUGGCCGUGUCCGACGAUUCGUUUAUUUGAUAGCCUU
--...((((...((((((..(((((....)))))..)))))).......((((.....)))).(((..(((....)))..))).....)))).. ( -26.20)
>DroSec_CAF1 63793 92 + 1
--UUCGGCUCCUGAGCUGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCAAUUCUUGGUCGUGUCCGACGAUUCGUUUAUUUGAUAGCCUU
--...((((...((((((..(((((....)))))..)))))).......((.((((.((((......)))).)))).)).........)))).. ( -27.70)
>DroSim_CAF1 63237 92 + 1
--UUCGGCUCCUGAGCUGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCAAUUCUUGGCCGUGUCCGACGAUUCGUUUAUUUGAUAGCCUU
--...((((...((((((..(((((....)))))..)))))).......((((.....)))).(((..(((....)))..))).....)))).. ( -28.60)
>DroEre_CAF1 67804 84 + 1
--UUCGGCUCCU--------GAGCUCCACAGCUCCACGGCUCCUUCCUUUCCAAUUCUUGGCCGUGUCCGACGAUUCGUUUAUUUGAUAGCCUU
--...((((...--------(((((....)))))(((((((..................)))))))......................)))).. ( -20.07)
>DroYak_CAF1 65757 86 + 1
CAUUCGGCUACU--------GAGCUUCUCAGCUCCACAGCUCCUUCCUUUCCAAUGCUUGGCCGUGUCCGACGAUUCGUUUAUUUGAUAGCCUU
.....(((((((--------(((...)))))..(((.(((...............))))))..(((..(((....)))..)))....))))).. ( -16.26)
>consensus
__UUCGGCUCCUGAG_UGCUGAGCUGCUCAGCUCCACAGCUCCUUCCUUGCCAAUUCUUGGCCGUGUCCGACGAUUCGUUUAUUUGAUAGCCUU
.....((((...((((((..(((((....)))))..)))))).......((((.....)))).(((..(((....)))..))).....)))).. (-16.66 = -19.30 +   2.64)

alignment

secondary structure

dotplot

Window 4

Location	23,858,255 – 23,858,347
Length	92
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	90.11
Mean single sequence MFE	-29.44
Consensus MFE	-21.52
Energy contribution	-21.56
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-3.12
Structure conservation index	0.73
SVM decision value	1.58
SVM RNA-class probability	0.965502
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23858255 92 - 27905053
AAGGCUAUCAAAUAAACGAAUCGUCGGACACGGCCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAACUCAGGAGCCGAA--
..((((.((.......(((....)))......((((.....))))...))..(((.(((.(((((....))))).))).)))...))))...-- ( -27.50)
>DroSec_CAF1 63793 92 - 1
AAGGCUAUCAAAUAAACGAAUCGUCGGACACGACCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAGCUCAGGAGCCGAA--
..((((.((.......(((.((((((....))))...)).))).........(((((((.(((((....))))).))))))).))))))...-- ( -33.60)
>DroSim_CAF1 63237 92 - 1
AAGGCUAUCAAAUAAACGAAUCGUCGGACACGGCCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCAGCUCAGGAGCCGAA--
..((((.((.......(((....)))......((((.....))))...))..(((((((.(((((....))))).)))))))...))))...-- ( -34.10)
>DroEre_CAF1 67804 84 - 1
AAGGCUAUCAAAUAAACGAAUCGUCGGACACGGCCAAGAAUUGGAAAGGAAGGAGCCGUGGAGCUGUGGAGCUC--------AGGAGCCGAA--
..((((.((.......(((....)))..(((((((.....((....))....).))))))(((((....)))))--------.))))))...-- ( -25.90)
>DroYak_CAF1 65757 86 - 1
AAGGCUAUCAAAUAAACGAAUCGUCGGACACGGCCAAGCAUUGGAAAGGAAGGAGCUGUGGAGCUGAGAAGCUC--------AGUAGCCGAAUG
..((((((........(((....)))..(((((((.....((....))....).))))))(((((....)))))--------.))))))..... ( -26.10)
>consensus
AAGGCUAUCAAAUAAACGAAUCGUCGGACACGGCCAAGAAUUGGCAAGGAAGGAGCUGUGGAGCUGAGCAGCUCAGCA_CUCAGGAGCCGAA__
..((((..........(((....)))..(((((((.....((....))....).))))))(((((....)))))...........))))..... (-21.52 = -21.56 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:14 2006