Locus 3059

Sequence ID	2R_DroMel_CAF1
Location	10,524,787 – 10,524,941
Length	154
Max. P	0.989515

overview

Window 7

Location	10,524,787 – 10,524,901
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.05
Mean single sequence MFE	-23.92
Consensus MFE	-21.84
Energy contribution	-21.68
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.80
Structure conservation index	0.91
SVM decision value	2.17
SVM RNA-class probability	0.989515
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10524787 114 - 20766785
ACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGUUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAAAAAUCGUUUCUGAAAAAUUGAAGCCAAAGCA------ACGGCC
.........((..(((....((.(((((.(((((((.....((((..(((......)))..)))).))))))).))))).))(((((.........)))))....)))------...)). ( -24.30)
>DroSec_CAF1 25671 114 - 1
ACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGCUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAAAAAUCGUUUCUGAAAAAUUGAAGCCAAAGCA------ACGACC
.......(((...(((....((.(((((.(((((((.....((((..(((......)))..)))).))))))).))))).))(((((.........)))))....)))------.))).. ( -23.40)
>DroSim_CAF1 21855 114 - 1
ACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGCUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAAAAAUCGUUUCUGAAAAAUUGAAGCCAAAGCA------ACGGCC
.........((..(((....((.(((((.(((((((.....((((..(((......)))..)))).))))))).))))).))(((((.........)))))....)))------...)). ( -24.30)
>DroEre_CAF1 27914 114 - 1
ACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGCUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAAAAAUCGUUUCUGAAAAAUUGAAGCCAAAGCA------AUAGCC
.........((..(((....((.(((((.(((((((.....((((..(((......)))..)))).))))))).))))).))(((((.........)))))....)))------...)). ( -23.20)
>DroYak_CAF1 25971 120 - 1
ACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGCUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAGAAAUCGUUUCUGAAAAAUUGAAGCCAAAGCAACAGCAACAGCC
.........((..((((...(((.....))).))))((((.((....(((......))).(((((((.......(((((.....)))))....)))))))......)).))))....)). ( -24.40)
>consensus
ACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGCUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAAAAAUCGUUUCUGAAAAAUUGAAGCCAAAGCA______ACGGCC
.............(((....((.(((((.(((((((.....((((..(((......)))..)))).))))))).))))).))(((((.........)))))....)))............ (-21.84 = -21.68 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	10,524,821 – 10,524,941
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	99.33
Mean single sequence MFE	-28.50
Consensus MFE	-27.52
Energy contribution	-27.72
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.97
SVM decision value	0.75
SVM RNA-class probability	0.840513
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10524821 120 + 20766785
UUUUUGUUUUCGCAUUGAAGUGCAUUUUAUUGCGAUUCAUCAACUGCAAAAGCAAAACUCGAGUGCAUUGCGAUUUGUGUUGUUCGAGAUGUGCGAGGUAUUUAAUUAAUUUGAAAAUAA
.(((((((((.(((.((((.((((......)))).)))).....))).)))))))))((((...((((..(((..........)))..)))).))))...(((((.....)))))..... ( -27.90)
>DroSec_CAF1 25705 120 + 1
UUUUUGUUUUCGCAUUGAAGUGCAUUUUAUUGCGAUUCAUCAGCUGCAAAAGCAAAACUCGAGUGCAUUGCGAUUUGUGUUGUUCGAGAUGUGCGAGGUAUUUAAUUAAUUUGAAAAUAA
...((((((((((..((((.((((......)))).))))...))(((....(((...(((((..((((........))))...)))))...)))...)))............)))))))) ( -28.70)
>DroSim_CAF1 21889 120 + 1
UUUUUGUUUUCGCAUUGAAGUGCAUUUUAUUGCGAUUCAUCAGCUGCAAAAGCAAAACUCGAGUGCAUUGCGAUUUGUGUUGUUCGAGAUGUGCGAGGUAUUUAAUUAAUUUGAAAAUAA
...((((((((((..((((.((((......)))).))))...))(((....(((...(((((..((((........))))...)))))...)))...)))............)))))))) ( -28.70)
>DroEre_CAF1 27948 120 + 1
UUUUUGUUUUCGCAUUGAAGUGCAUUUUAUUGCGAUUCAUCAGCUGCAAAAGCAAAACUCGAGUGCAUUGCGAUUUGUGUUGUUCGAGAUGUGCGAGGUAUUUAAUUAAUUUGAAAAUAA
...((((((((((..((((.((((......)))).))))...))(((....(((...(((((..((((........))))...)))))...)))...)))............)))))))) ( -28.70)
>DroYak_CAF1 26011 120 + 1
UUUCUGUUUUCGCAUUGAAGUGCAUUUUAUUGCGAUUCAUCAGCUGCAAAAGCAAAACUCGAGUGCAUUGCGAUUUGUGUUGUUCGAGAUGUGCGAGGUAUUUAAUUAAUUUGAAAAUAA
....(((((((((..((((.((((......)))).))))...))(((....(((...(((((..((((........))))...)))))...)))...)))............))))))). ( -28.50)
>consensus
UUUUUGUUUUCGCAUUGAAGUGCAUUUUAUUGCGAUUCAUCAGCUGCAAAAGCAAAACUCGAGUGCAUUGCGAUUUGUGUUGUUCGAGAUGUGCGAGGUAUUUAAUUAAUUUGAAAAUAA
....(((((((((..((((.((((......)))).))))...))(((....(((...(((((..((((........))))...)))))...)))...)))............))))))). (-27.52 = -27.72 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	10,524,821 – 10,524,941
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.33
Mean single sequence MFE	-19.00
Consensus MFE	-18.88
Energy contribution	-18.72
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.46
Structure conservation index	0.99
SVM decision value	0.93
SVM RNA-class probability	0.884494
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10524821 120 - 20766785
UUAUUUUCAAAUUAAUUAAAUACCUCGCACAUCUCGAACAACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGUUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAAAAA
........................(((((.........((((.((((..((((.((......)).)))).))))..)))).((((..(((......)))..)))).)))))......... ( -20.10)
>DroSec_CAF1 25705 120 - 1
UUAUUUUCAAAUUAAUUAAAUACCUCGCACAUCUCGAACAACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGCUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAAAAA
.......................((((..(((..(((..........)))..)))....))))(((((.(((((((.....((((..(((......)))..)))).))))))).))))). ( -18.70)
>DroSim_CAF1 21889 120 - 1
UUAUUUUCAAAUUAAUUAAAUACCUCGCACAUCUCGAACAACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGCUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAAAAA
.......................((((..(((..(((..........)))..)))....))))(((((.(((((((.....((((..(((......)))..)))).))))))).))))). ( -18.70)
>DroEre_CAF1 27948 120 - 1
UUAUUUUCAAAUUAAUUAAAUACCUCGCACAUCUCGAACAACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGCUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAAAAA
.......................((((..(((..(((..........)))..)))....))))(((((.(((((((.....((((..(((......)))..)))).))))))).))))). ( -18.70)
>DroYak_CAF1 26011 120 - 1
UUAUUUUCAAAUUAAUUAAAUACCUCGCACAUCUCGAACAACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGCUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAGAAA
.......................((((..(((..(((..........)))..)))....))))(((((.(((((((.....((((..(((......)))..)))).))))))).))))). ( -18.80)
>consensus
UUAUUUUCAAAUUAAUUAAAUACCUCGCACAUCUCGAACAACACAAAUCGCAAUGCACUCGAGUUUUGCUUUUGCAGCUGAUGAAUCGCAAUAAAAUGCACUUCAAUGCGAAAACAAAAA
.......................((((..(((..(((..........)))..)))....))))(((((.(((((((.....((((..(((......)))..)))).))))))).))))). (-18.88 = -18.72 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:18 2006