Locus 6140

Sequence ID	3L_DroMel_CAF1
Location	16,257,419 – 16,257,595
Length	176
Max. P	0.997912

overview

Window 2

Location	16,257,419 – 16,257,528
Length	109
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	88.79
Mean single sequence MFE	-29.60
Consensus MFE	-28.90
Energy contribution	-28.77
Covariance contribution	-0.12
Combinations/Pair	1.10
Mean z-score	-1.32
Structure conservation index	0.98
SVM decision value	0.38
SVM RNA-class probability	0.714427
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16257419 109 + 23771897
CGAUAUGUUCACCUUCGCUGAACCGAAAAAGGGGGCACAGAUAGCGGGAAUUUCCACGCACGUUUUUCUUUUUGUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCA
...........((((((......)))...)))((((.......(((((.....)).)))........................((((((((....)))))))).)))). ( -30.80)
>DroSec_CAF1 8859 108 + 1
CGAUAUGUUCACCUUCGCUGAACCGAAAA-AAGGGCACAGAUAGCGGGAAUUUCCACGCACGUUUUCUCUUUUCUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCA
......(((((.......)))))......-..((((.......(((((.....)).)))........................((((((((....)))))))).)))). ( -30.60)
>DroSim_CAF1 7313 108 + 1
CGAUAUGUUCACCUUCGCUGAACCGAAAA-GAGGGCACAGAUAGCGGGAAUUUCCACGCACGUUUUUCUUUUCGUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCA
......(((((.......)))))......-..((((.......(((((.....)).)))........................((((((((....)))))))).)))). ( -30.60)
>DroEre_CAF1 8769 96 + 1
CGAUAUGUUCACCUUCGCUGAACCGAAAA-GAGGGCACAAAU-GCGGGAAUUUCCACGCACGUUUU-----------UCCCUUCGCGCUUCAAGUGGAGCACACGCCCA
......(((((.......)))))......-..((((.....(-(((((.....)).))))......-----------.......(.(((((....))))).)..)))). ( -26.40)
>consensus
CGAUAUGUUCACCUUCGCUGAACCGAAAA_GAGGGCACAGAUAGCGGGAAUUUCCACGCACGUUUUUCUUUUUGUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCA
......(((((.......))))).........((((.......(((((.....)).))).........................(((((((....)))))))..)))). (-28.90 = -28.77 +  -0.12)

alignment

secondary structure

dotplot

Window 3

Location	16,257,453 – 16,257,567
Length	114
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	86.84
Mean single sequence MFE	-32.55
Consensus MFE	-28.21
Energy contribution	-27.90
Covariance contribution	-0.31
Combinations/Pair	1.20
Mean z-score	-1.43
Structure conservation index	0.87
SVM decision value	0.13
SVM RNA-class probability	0.596595
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16257453 114 + 23771897
GCACAGAUAGCGGGAAUUUCCACGCACGUUUUUCUUUUUGUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCAGCUUUUGAGCUGAUUCUACUCCUCGAGUGGUUGCUUCGC
(((((((..(((((.....)).)))(((..........)))......))))))).....((((((((......(((((....)))))...((((((...)))))).)))))))) ( -32.10)
>DroSec_CAF1 8892 114 + 1
GCACAGAUAGCGGGAAUUUCCACGCACGUUUUCUCUUUUCUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCAGCUCUUGAGUUGAUUCCACUCCUCGAGUGGUUGCUUCGC
(((((((..(((((.....)).)))..(......)............))))))).....((((((((......(((((....)))))...((((((...)))))).)))))))) ( -32.20)
>DroSim_CAF1 7346 114 + 1
GCACAGAUAGCGGGAAUUUCCACGCACGUUUUUCUUUUCGUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCAGCUCUUGAGUUGAUUCCACUCCUCGAGUGGUUGCUUCGC
(((((((..(((((.....)).)))(((..........)))......))))))).....((((((((......(((((....)))))...((((((...)))))).)))))))) ( -34.10)
>DroEre_CAF1 8802 102 + 1
GCACAAAU-GCGGGAAUUUCCACGCACGUUUU-----------UCCCUUCGCGCUUCAAGUGGAGCACACGCCCAGCACUUGAGCUGAUUCUGCUCCUGAAGUGGUUGCUCCGC
(((....(-(((((.....)).))))......-----------........(((((((...((((((......((((......))))....)))))))))))))..)))..... ( -31.80)
>consensus
GCACAGAUAGCGGGAAUUUCCACGCACGUUUUUCUUUUUGUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCAGCUCUUGAGCUGAUUCCACUCCUCGAGUGGUUGCUUCGC
((.......(((((.....)).))).........................(((((((....)))))))..)).(((((....)))))...((((((...))))))......... (-28.21 = -27.90 +  -0.31)

alignment

secondary structure

dotplot

Window 4

Location	16,257,488 – 16,257,595
Length	107
Sequences	4
Columns	119
Reading direction	forward
Mean pairwise identity	81.87
Mean single sequence MFE	-26.95
Consensus MFE	-23.19
Energy contribution	-22.88
Covariance contribution	-0.31
Combinations/Pair	1.24
Mean z-score	-2.94
Structure conservation index	0.86
SVM decision value	2.96
SVM RNA-class probability	0.997912
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16257488 107 + 23771897
UUUUGUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCAGCUUUUGAGCUGAUUCUACUCCUCGAGUGGUUGCUUCGCGUUUUCCCCC--AU-UUUCCA---------UACAAAUUUU
.(((((.........(((((((....)))))))((((.(((((....)))))...((((((...)))))).......))))........--..-......---------.))))).... ( -27.80)
>DroSec_CAF1 8927 109 + 1
UUUUCUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCAGCUCUUGAGUUGAUUCCACUCCUCGAGUGGUUGCUUCGCGUUUUCCCCCCCUU-UUUCCA---------UACAAAUUUU
...............(((((((....)))))))((((.(((((....)))))...((((((...)))))).......))))............-......---------.......... ( -26.80)
>DroSim_CAF1 7381 110 + 1
UUUCGUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCAGCUCUUGAGUUGAUUCCACUCCUCGAGUGGUUGCUUCGCGUUUUCCCCCCCUUUUUUCCA---------UACAAAUUUU
...............(((((((....)))))))((((.(((((....)))))...((((((...)))))).......))))...................---------.......... ( -26.80)
>DroEre_CAF1 8833 110 + 1
--------UCCCUUCGCGCUUCAAGUGGAGCACACGCCCAGCACUUGAGCUGAUUCUGCUCCUGAAGUGGUUGCUCCGCGAUUUCCCCCAUUU-UCUACACAGAUUUUCCACAAAUUUU
--------.....((((((((((...((((((......((((......))))....))))))))))))((.....))))))............-......................... ( -26.40)
>consensus
UUUUGUUUUCCUUUUGUGUUCCAAGUGGAGCACACGCCCAGCUCUUGAGCUGAUUCCACUCCUCGAGUGGUUGCUUCGCGUUUUCCCCCCCUU_UUUCCA_________UACAAAUUUU
...............(((((((....))))))).(((.(((((....)))))...((((((...)))))).......)))....................................... (-23.19 = -22.88 +  -0.31)

alignment

secondary structure

dotplot

Window 5

Location	16,257,488 – 16,257,595
Length	107
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	81.87
Mean single sequence MFE	-28.06
Consensus MFE	-20.55
Energy contribution	-20.55
Covariance contribution	0.00
Combinations/Pair	1.18
Mean z-score	-2.07
Structure conservation index	0.73
SVM decision value	1.10
SVM RNA-class probability	0.914482
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16257488 107 - 23771897
AAAAUUUGUA---------UGGAAA-AU--GGGGGAAAACGCGAAGCAACCACUCGAGGAGUAGAAUCAGCUCAAAAGCUGGGCGUGUGCUCCACUUGGAACACAAAAGGAAAACAAAA
....(((((.---------......-..--.((((...((((.........((((...))))....((((((....))))))))))...))))..(((.....))).......))))). ( -23.90)
>DroSec_CAF1 8927 109 - 1
AAAAUUUGUA---------UGGAAA-AAGGGGGGGAAAACGCGAAGCAACCACUCGAGGAGUGGAAUCAACUCAAGAGCUGGGCGUGUGCUCCACUUGGAACACAAAAGGAAAAGAAAA
....(((((.---------......-(((..((((...((((..(((..((((((...))))))..((.......)))))..))))...)))).))).....)))))............ ( -28.40)
>DroSim_CAF1 7381 110 - 1
AAAAUUUGUA---------UGGAAAAAAGGGGGGGAAAACGCGAAGCAACCACUCGAGGAGUGGAAUCAACUCAAGAGCUGGGCGUGUGCUCCACUUGGAACACAAAAGGAAAACGAAA
....(((((.---------.......(((..((((...((((..(((..((((((...))))))..((.......)))))..))))...)))).))).....)))))............ ( -27.82)
>DroEre_CAF1 8833 110 - 1
AAAAUUUGUGGAAAAUCUGUGUAGA-AAAUGGGGGAAAUCGCGGAGCAACCACUUCAGGAGCAGAAUCAGCUCAAGUGCUGGGCGUGUGCUCCACUUGAAGCGCGAAGGGA--------
....(((((((....((((((....-.............))))))....)).(((((((((((.(.(((((......)))))...).))))))...))))).)))))....-------- ( -32.13)
>consensus
AAAAUUUGUA_________UGGAAA_AAGGGGGGGAAAACGCGAAGCAACCACUCGAGGAGUAGAAUCAACUCAAGAGCUGGGCGUGUGCUCCACUUGGAACACAAAAGGAAAACAAAA
...............................((((...(((((......((((((...((((.......))))..))).))).))))).))))..(((.....)))............. (-20.55 = -20.55 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:08 2006