Locus 620

Sequence ID	3R_DroMel_CAF1
Location	2,292,384 – 2,292,556
Length	172
Max. P	0.997503

overview

Window 7

Location	2,292,384 – 2,292,491
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.98
Mean single sequence MFE	-29.84
Consensus MFE	-14.60
Energy contribution	-14.64
Covariance contribution	0.04
Combinations/Pair	1.26
Mean z-score	-2.85
Structure conservation index	0.49
SVM decision value	2.87
SVM RNA-class probability	0.997503
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2292384 107 + 27905053
UAAGCCGCGUUUG---------CCCAAAAACGGUCAACA-GACCACAUUCAACGACCACUUGGC--CCAUGUCGC-UGGCAGGACCGCCAAUGUAAUAAUAGCAAAGGCAAACAGCAGCG
...((.(((((((---------((.......((((....-)))).............(((((((--((.(((...-..)))))...))))).))............))))))).)).)). ( -31.70)
>DroSec_CAF1 28642 107 + 1
UAAGCCGCGUUUG---------CCCAAAAACGGUCAAAC-GACCACAUUCAACGACCACUUGGU--CCAUGUCGC-UGGCAGGACCGCCAAUAUAAUAAUAGCAAAGGCAAACAGCAGCG
...((.(((((((---------((.......((((....-)))).................(((--((.(((...-..))))))))....................))))))).)).)). ( -33.80)
>DroSim_CAF1 30268 108 + 1
UAAGCCGCGUUUG---------CCCAAAAACGGUCAAACUUACCACAUUCAACGACCACUUGGU--CCAUGUCGC-UGGCAGGACCGCCAAUAUAAUAAUAGCAAAGGCAAACAGCAGCG
...((.(((((((---------((.......((((..................))))....(((--((.(((...-..))))))))....................))))))).)).)). ( -32.27)
>DroYak_CAF1 27447 96 + 1
UAAGCUGCGUUUGGCCGUUUUGACCAAAAACGGUCAACC-GACCACAUUCAACGACCACUUGG-----------------------GCCAAUAUAAUAAUAGCAAAAGCAAACUGCAGCG
...(((((..(((((((((((.....)))))((((....-))))..................)-----------------------)))))..........((....)).....))))). ( -30.10)
>DroAna_CAF1 28219 103 + 1
UAAGCCGCGUUUCA--------CCCAAAAACGGUCAAAU-GACCACAUUCAUCGGCCGCUUGGUGUCCACGGACCACGUUAUCCCAGCCAAUAUAAUAAUAACAAAGGCAAA--------
(((((.((((((..--------.....))))((((....-))))..........)).)))))(((((....)).))).........(((.................)))...-------- ( -21.33)
>consensus
UAAGCCGCGUUUG_________CCCAAAAACGGUCAAAC_GACCACAUUCAACGACCACUUGGU__CCAUGUCGC_UGGCAGGACCGCCAAUAUAAUAAUAGCAAAGGCAAACAGCAGCG
...(((..(((....................((((.....))))...............(((((.....((((....)))).....))))).........)))...)))........... (-14.60 = -14.64 +   0.04)

alignment

secondary structure

dotplot

Window 8

Location	2,292,384 – 2,292,491
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.98
Mean single sequence MFE	-37.90
Consensus MFE	-18.15
Energy contribution	-18.95
Covariance contribution	0.80
Combinations/Pair	1.15
Mean z-score	-2.69
Structure conservation index	0.48
SVM decision value	2.48
SVM RNA-class probability	0.994414
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2292384 107 - 27905053
CGCUGCUGUUUGCCUUUGCUAUUAUUACAUUGGCGGUCCUGCCA-GCGACAUGG--GCCAAGUGGUCGUUGAAUGUGGUC-UGUUGACCGUUUUUGGG---------CAAACGCGGCUUA
.(((((.((((((((..((.......(((((((((....)))).-.((((...(--(((....)))))))))))))((((-....))))))....)))---------))))))))))... ( -42.20)
>DroSec_CAF1 28642 107 - 1
CGCUGCUGUUUGCCUUUGCUAUUAUUAUAUUGGCGGUCCUGCCA-GCGACAUGG--ACCAAGUGGUCGUUGAAUGUGGUC-GUUUGACCGUUUUUGGG---------CAAACGCGGCUUA
.(((((.((((((((..((((.........))))((((..((..-((.((((.(--(((....)))).....)))).)).-))..))))......)))---------))))))))))... ( -41.00)
>DroSim_CAF1 30268 108 - 1
CGCUGCUGUUUGCCUUUGCUAUUAUUAUAUUGGCGGUCCUGCCA-GCGACAUGG--ACCAAGUGGUCGUUGAAUGUGGUAAGUUUGACCGUUUUUGGG---------CAAACGCGGCUUA
.(((((.((((((((..((((.........))))((((..((..-((.((((.(--(((....)))).....)))).))..))..))))......)))---------))))))))))... ( -42.10)
>DroYak_CAF1 27447 96 - 1
CGCUGCAGUUUGCUUUUGCUAUUAUUAUAUUGGC-----------------------CCAAGUGGUCGUUGAAUGUGGUC-GGUUGACCGUUUUUGGUCAAAACGGCCAAACGCAGCUUA
.(((((.(.(..(((..((((.........))))-----------------------..)))..).)........(((((-(.(((((((....)))))))..))))))...)))))... ( -34.30)
>DroAna_CAF1 28219 103 - 1
--------UUUGCCUUUGUUAUUAUUAUAUUGGCUGGGAUAACGUGGUCCGUGGACACCAAGCGGCCGAUGAAUGUGGUC-AUUUGACCGUUUUUGGG--------UGAAACGCGGCUUA
--------...(((.............(((((((((((((......)))).(((...)))..)))))))))...((((((-....))))(((((....--------.))))))))))... ( -29.90)
>consensus
CGCUGCUGUUUGCCUUUGCUAUUAUUAUAUUGGCGGUCCUGCCA_GCGACAUGG__ACCAAGUGGUCGUUGAAUGUGGUC_GUUUGACCGUUUUUGGG_________CAAACGCGGCUUA
.(((((.(((((((..((.((....))))..))).......................(((((((((((................))))))..)))))...........)))))))))... (-18.15 = -18.95 +   0.80)

alignment

secondary structure

dotplot

Window 9

Location	2,292,414 – 2,292,530
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.42
Mean single sequence MFE	-34.33
Consensus MFE	-20.90
Energy contribution	-21.70
Covariance contribution	0.80
Combinations/Pair	1.18
Mean z-score	-1.81
Structure conservation index	0.61
SVM decision value	0.30
SVM RNA-class probability	0.679897
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2292414 116 + 27905053
GACCACAUUCAACGACCACUUGGC--CCAUGUCGC-UGGCAGGACCGCCAAUGUAAUAAUAGCAAAGGCAAACAGCAGCGAUAUGGGAUCCGAUUUGGAUCCAAUGCGGGUCGAGUGCU-
................((((((((--(((((((((-((.(.(....(((..(((.......)))..)))...).)))))))))).((((((.....)))))).....))))))))))..- ( -44.70)
>DroSec_CAF1 28672 116 + 1
GACCACAUUCAACGACCACUUGGU--CCAUGUCGC-UGGCAGGACCGCCAAUAUAAUAAUAGCAAAGGCAAACAGCAGCGAUAUGGGAUCCGAUUUGGAUCCAAUGCGGGUCGAGUGCU-
((((.((((....((((....)))--)((((((((-((((......)))............((....)).......)))))))))((((((.....))))))))))..)))).......- ( -40.90)
>DroSim_CAF1 30299 116 + 1
UACCACAUUCAACGACCACUUGGU--CCAUGUCGC-UGGCAGGACCGCCAAUAUAAUAAUAGCAAAGGCAAACAGCAGCGAUAUGGGAUCCGAUUUGGAUCCAAUGCGGGUCGAGUGCU-
................((((((..--(((((((((-((((......)))............((....)).......)))))))).((((((.....)))))).....))..))))))..- ( -40.10)
>DroYak_CAF1 27486 96 + 1
GACCACAUUCAACGACCACUUGG-----------------------GCCAAUAUAAUAAUAGCAAAAGCAAACUGCAGCGAUAUGGGAUCCGAUUUGAAUCCAAUGCGGGUCGAGUGCU-
................(((((((-----------------------.((..................((.....)).(((...((((.((......)).)))).))))).)))))))..- ( -20.10)
>DroAna_CAF1 28250 106 + 1
GACCACAUUCAUCGGCCGCUUGGUGUCCACGGACCACGUUAUCCCAGCCAAUAUAAUAAUAACAAAGGCAAA---------UAUGGGAUCCGAUUUGCAC-----UUGGGUCGAGUGCCA
...........((((((.(..(((((...((((........((((((((.................)))...---------..)))))))))....))))-----).)))))))...... ( -25.83)
>consensus
GACCACAUUCAACGACCACUUGGU__CCAUGUCGC_UGGCAGGACCGCCAAUAUAAUAAUAGCAAAGGCAAACAGCAGCGAUAUGGGAUCCGAUUUGGAUCCAAUGCGGGUCGAGUGCU_
.....(((((.....(((.(((((.....((((....)))).....)))))..........((....))..............)))((((((..(((....)))..)))))))))))... (-20.90 = -21.70 +   0.80)

alignment

secondary structure

dotplot

Window 0

Location	2,292,451 – 2,292,556
Length	105
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	92.38
Mean single sequence MFE	-34.28
Consensus MFE	-25.54
Energy contribution	-25.60
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-2.31
Structure conservation index	0.74
SVM decision value	0.35
SVM RNA-class probability	0.701975
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2292451 105 + 27905053
AGGACCGCCAAUGUAAUAAUAGCAAAGGCAAACAGCAGCGAUAUGGGAUCCGAUUUGGAUCCAAUGCGGGUCGAGUGCUGGUGCAUCCGCAUCCAUAUGUGGACU
.(.((((((..(((.......)))..)))....((((.((((...((((((.....)))))).......))))..))))))).).(((((((....))))))).. ( -36.60)
>DroSec_CAF1 28709 105 + 1
AGGACCGCCAAUAUAAUAAUAGCAAAGGCAAACAGCAGCGAUAUGGGAUCCGAUUUGGAUCCAAUGCGGGUCGAGUGCUGGUCCAUCCGCAUCCAUAUGUGGACU
.((((((((.................)))....((((.((((...((((((.....)))))).......))))..))))))))).(((((((....))))))).. ( -38.53)
>DroSim_CAF1 30336 105 + 1
AGGACCGCCAAUAUAAUAAUAGCAAAGGCAAACAGCAGCGAUAUGGGAUCCGAUUUGGAUCCAAUGCGGGUCGAGUGCUGGUGCAUCCGCAUCCAUACCUGGACU
....((((.............((....((.....)).))......((((((.....))))))...))))(((.((...((((((....))).)))...)).))). ( -30.60)
>DroYak_CAF1 27509 99 + 1
------GCCAAUAUAAUAAUAGCAAAAGCAAACUGCAGCGAUAUGGGAUCCGAUUUGAAUCCAAUGCGGGUCGAGUGCUGGUGCAUCCGUAUCCAUAUGUGGCAU
------((((.((((............((.....)).(.(((((((((((((..(((....)))..))))))..((((....)))))))))))).)))))))).. ( -31.40)
>consensus
AGGACCGCCAAUAUAAUAAUAGCAAAGGCAAACAGCAGCGAUAUGGGAUCCGAUUUGGAUCCAAUGCGGGUCGAGUGCUGGUGCAUCCGCAUCCAUAUGUGGACU
.......(((...........((....((.....)).)).((((((((((((..(((....)))..))))))..((((.((.....)))))))))))).)))... (-25.54 = -25.60 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:42 2006