Locus 3359

Sequence ID	2R_DroMel_CAF1
Location	11,388,382 – 11,388,528
Length	146
Max. P	0.964396

overview

Window 0

Location	11,388,382 – 11,388,488
Length	106
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.95
Mean single sequence MFE	-43.48
Consensus MFE	-32.31
Energy contribution	-32.73
Covariance contribution	0.42
Combinations/Pair	1.27
Mean z-score	-1.91
Structure conservation index	0.74
SVM decision value	1.57
SVM RNA-class probability	0.964396
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11388382 106 - 20766785
CUGUCGCUCGAGGCAGCCGUUGAAGUACGCCAAGUGCGUGGGCGGCUGCGGCAACCAGUGCUGCGCGGCCAAAAUUGUGAGACGGCGCAAGGUGAGUGAA-------UCUGAA-------
...(((((((..((.((((((....(((((.....)))))(((.((.((((((.....)))))))).)))..........))))))))....))))))).-------......------- ( -45.30)
>DroVir_CAF1 6319 116 - 1
CUGCCGCUCCAGGCAGCCGCUGAAGUACGCCAAAUGCGUCGGCGGCUGCGGCAAUCAGUGCUGUGCGGCCAAAAUCGUGCGGAGGCGCAAGGUAAGUGCC----AAAUAUGAUUCCAUUA
..(((((.....(((((((((((....(((.....))))))))))))))((((.....))))..)))))...(((((((....(((((.......)))))----...)))))))...... ( -48.20)
>DroGri_CAF1 5462 117 - 1
CUGCCGCUCGAGGCAGCCGCUGAAGUACGCCAAAUGCGUUGGCGGCUGCGGCAAUCAAUGCUGUGCGGCCAAAAUAGUGCGAAGGCGCAAGGUAAGUGCCCCCAAAAUAU---CCACACA
..(((((.(...(((((((((.....((((.....)))).)))))))))((((.....))))).))))).......((((....))))..(((....)))..........---....... ( -45.30)
>DroWil_CAF1 5267 108 - 1
UUGCCGUUCCAGGCAGCCGCUGAAAUAUGCCAAAUGCGUGGGCGGCUGUGGCAAUCAAUGCUGUGCAGCAAAGAUUGUCAGAAGGCGCAAGGUAAGCGAA----AAAUCUCU--------
..(((.(((...(((((((((....(((((.....))))))))))))))(((((((..((((....))))..))))))).))))))((.......))...----........-------- ( -40.50)
>DroMoj_CAF1 5955 116 - 1
CUGCCGCUCCAGGCAGCCGCUGAAGUACGCCAAAUGCGUCGGCGGUUGCGGCAAUCAAUGCUGCGCGGCCAAAAUUGUGCGAAGACGCAAGGUAAGUGCA----AAAAAUUAUUCCAUUA
..(((((.....(((((((((((....(((.....))))))))))))))((((.....))))..))))).....(((..(.....(....)....)..))----)............... ( -42.60)
>DroAna_CAF1 4608 102 - 1
CUGCCGAUCCCGGCAACCGCUCAAGUACGCCAAGUGCGUGGGAGGAUGUGGCAACCAGUGCUGCGCGGCGAAGAUUGUGCGGCGGCGCAAGGUGAGUGUG-------GC-----------
.(((((....))))).((((((......((((.((.(......).)).)))).(((.((((((((((.(((...)))))).)))))))..)))))))).)-------..----------- ( -39.00)
>consensus
CUGCCGCUCCAGGCAGCCGCUGAAGUACGCCAAAUGCGUGGGCGGCUGCGGCAAUCAAUGCUGCGCGGCCAAAAUUGUGCGAAGGCGCAAGGUAAGUGCA____AAAUAU_A________
..(((((.(...((((((((((....((((.....))))))))))))))((((.....))))).)))))....((..((((....))))..))........................... (-32.31 = -32.73 +   0.42)

alignment

secondary structure

dotplot

Window 1

Location	11,388,408 – 11,388,528
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	88.72
Mean single sequence MFE	-49.48
Consensus MFE	-42.29
Energy contribution	-42.63
Covariance contribution	0.34
Combinations/Pair	1.26
Mean z-score	-1.95
Structure conservation index	0.85
SVM decision value	0.68
SVM RNA-class probability	0.819602
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11388408 120 - 20766785
GUCGCAAGGAGCAGGUGCGCGAGUACUACACGGAGAACGACUGUCGCUCGAGGCAGCCGUUGAAGUACGCCAAGUGCGUGGGCGGCUGCGGCAACCAGUGCUGCGCGGCCAAAAUUGUGA
.((((((.((((.(((((....)))))...((.....))......))))..((((((((((.(.((((.....)))).).)))))))((((((.....))))))...)))....)))))) ( -51.00)
>DroVir_CAF1 6355 120 - 1
GUCGCAAGGAGCAGGUGCGUGAGUAUUACACGGAGAACGACUGCCGCUCCAGGCAGCCGCUGAAGUACGCCAAAUGCGUCGGCGGCUGCGGCAAUCAGUGCUGUGCGGCCAAAAUCGUGC
((((((.(((((.(((((....)))))....((((.....)).)))))))..(((((((((((....(((.....))))))))))))))((((.....)))).))))))........... ( -53.10)
>DroGri_CAF1 5499 120 - 1
GCCGCAAGGAGCAGGUGCGAGAGUAUUACACGGAGAACGACUGCCGCUCGAGGCAGCCGCUGAAGUACGCCAAAUGCGUUGGCGGCUGCGGCAAUCAAUGCUGUGCGGCCAAAAUAGUGC
((((((...(((((((((....)))))...........((.((((.(....)(((((((((.....((((.....)))).))))))))))))).))..)))).))))))........... ( -49.40)
>DroWil_CAF1 5295 120 - 1
GUCGGAAGGAGCAGGUGCGUGAGUAUUACACAGAGAACGAUUGCCGUUCCAGGCAGCCGCUGAAAUAUGCCAAAUGCGUGGGCGGCUGUGGCAAUCAAUGCUGUGCAGCAAAGAUUGUCA
...((((.(.((((((((....))))).(.....)......)))).))))..(((((((((....(((((.....))))))))))))))(((((((..((((....))))..))))))). ( -46.60)
>DroMoj_CAF1 5991 120 - 1
GUCGCAAGGAGCAGGUGCGUGAGUACUACACGGAGAACGACUGCCGCUCCAGGCAGCCGCUGAAGUACGCCAAAUGCGUCGGCGGUUGCGGCAAUCAAUGCUGCGCGGCCAAAAUUGUGC
..((((((((((.(((((....)))))....((((.....)).))))))).((((((((((((....(((.....))))))))))))((((((.....))))))...)))....))))). ( -53.30)
>DroAna_CAF1 4630 120 - 1
GUCGCAAGGAGCAGGUGCGCGAGUACUACACGGAGAACGACUGCCGAUCCCGGCAACCGCUCAAGUACGCCAAGUGCGUGGGAGGAUGUGGCAACCAGUGCUGCGCGGCGAAGAUUGUGC
(((((..(.(((((((((....))))).((((.........(((((....))))).((.((((.((((.....)))).)))).)).))))........)))).))))))........... ( -43.50)
>consensus
GUCGCAAGGAGCAGGUGCGUGAGUACUACACGGAGAACGACUGCCGCUCCAGGCAGCCGCUGAAGUACGCCAAAUGCGUGGGCGGCUGCGGCAAUCAAUGCUGCGCGGCCAAAAUUGUGC
(((((..(((((.(((((....)))))...((.....))......)))))..((((((((((....((((.....))))))))))))))((((.....))))..)))))........... (-42.29 = -42.63 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:37 2006