Locus 5054

Sequence ID	2R_DroMel_CAF1
Location	16,426,806 – 16,426,904
Length	98
Max. P	0.815013

overview

Window 6

Location	16,426,806 – 16,426,904
Length	98
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	81.52
Mean single sequence MFE	-30.00
Consensus MFE	-22.42
Energy contribution	-23.22
Covariance contribution	0.79
Combinations/Pair	1.13
Mean z-score	-1.89
Structure conservation index	0.75
SVM decision value	0.66
SVM RNA-class probability	0.815013
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16426806 98 + 20766785
C-------C-GCCCAACGCCCAUGCCACCAAAUUGGCAGCAAGUUGCGAAAAAAGGGUGGGCACUGAUAUUGCCGCGAUUAUGGUUAUUUCCAUAACACCACAGCC
.-------(-((....(((((.(((((......)))))((.....)).......)))))((((.......))))))).((((((......)))))).......... ( -31.00)
>DroSec_CAF1 102466 98 + 1
C-------C-GCCCAACGCCCAUGCCACCAAAUUGGCAGCAAGUUGCGAAAAAAGGGUGGGCACUGGUAUUGCCGCGAUUAUGGUUAUGGCCAUAACACCACCGCC
.-------(-((....(((((.(((((......)))))((.....)).......)))))((((.......))))))).(((((((....))))))).......... ( -32.40)
>DroSim_CAF1 98224 98 + 1
C-------C-GCCCAACGCCCGUGCCACCAAAUUGGCAGCAAGUUGCGAAAAAAGGGUGGGCACUGAUAUUGCCGCGAUUAUGGUUAUGGCUAUAACACCACCGCC
.-------(-((....(((((.(((((......)))))((.....)).......)))))((((.......))))))).(((((((....))))))).......... ( -30.00)
>DroEre_CAF1 102159 105 + 1
CCGCACACC-GCCCACCGCCCAUGCCACCAAAUUGGCAGCAAGUUGCGAAAAAAGGGUCGGCACUGAUAUUGCCGCGAUUAUGGUUAUGGCCAUAACACCACAAGC
..((....(-((.....((((.(((((......)))))((.....)).......)))).((((.......))))))).(((((((....)))))))........)) ( -30.40)
>DroYak_CAF1 102857 98 + 1
C-------A-GCCCACCGCCCAUGCCACCAAAUUGGCAGCAAGUUGCGAAAAAAGGGUGGGUACUGAUAUAGCCGCGAUUAUGGUUAUGGCCAUAACACCACAGCC
(-------(-(..(.((((((.(((((......)))))((.....)).......)))))))..))).....((.(.(.(((((((....)))))))...).).)). ( -30.90)
>DroAna_CAF1 97413 84 + 1
C-------UUGCCCUAACCCUAUAUC--------CCAAGGAACUUGCGAAAAAUGGGUGGGCAUUGAUAUUCCAACGAUUAUGGUU--UGCCAUAACUCGA-----
.-------.(((((..((((....((--------.((((...)))).)).....)))))))))............(((((((((..--..)))))).))).----- ( -25.30)
>consensus
C_______C_GCCCAACGCCCAUGCCACCAAAUUGGCAGCAAGUUGCGAAAAAAGGGUGGGCACUGAUAUUGCCGCGAUUAUGGUUAUGGCCAUAACACCACAGCC
..........((((...((((.(((((......)))))((.....)).......))))))))..............(.(((((((....))))))))......... (-22.42 = -23.22 +   0.79)

alignment

secondary structure

dotplot

Window 7

Location	16,426,806 – 16,426,904
Length	98
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	81.52
Mean single sequence MFE	-35.78
Consensus MFE	-21.54
Energy contribution	-23.07
Covariance contribution	1.53
Combinations/Pair	1.04
Mean z-score	-2.03
Structure conservation index	0.60
SVM decision value	0.25
SVM RNA-class probability	0.652414
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16426806 98 - 20766785
GGCUGUGGUGUUAUGGAAAUAACCAUAAUCGCGGCAAUAUCAGUGCCCACCCUUUUUUCGCAACUUGCUGCCAAUUUGGUGGCAUGGGCGUUGGGC-G-------G
.((((((((..(((((......)))))))))))))........((((((.........(((....(((..((.....))..)))...))).)))))-)-------. ( -37.20)
>DroSec_CAF1 102466 98 - 1
GGCGGUGGUGUUAUGGCCAUAACCAUAAUCGCGGCAAUACCAGUGCCCACCCUUUUUUCGCAACUUGCUGCCAAUUUGGUGGCAUGGGCGUUGGGC-G-------G
((((.(((((((...(((..............)))))))))).))))(.(((......(((....(((..((.....))..)))...)))..))).-)-------. ( -37.14)
>DroSim_CAF1 98224 98 - 1
GGCGGUGGUGUUAUAGCCAUAACCAUAAUCGCGGCAAUAUCAGUGCCCACCCUUUUUUCGCAACUUGCUGCCAAUUUGGUGGCACGGGCGUUGGGC-G-------G
((((.(((((((...(((..............)))))))))).))))(.(((......(((....(((..((.....))..)))...)))..))).-)-------. ( -33.84)
>DroEre_CAF1 102159 105 - 1
GCUUGUGGUGUUAUGGCCAUAACCAUAAUCGCGGCAAUAUCAGUGCCGACCCUUUUUUCGCAACUUGCUGCCAAUUUGGUGGCAUGGGCGGUGGGC-GGUGUGCGG
((((((.(((((((((......)))))).))).)))).....(..(((.(((.....((((....(((..((.....))..)))...)))).))))-))..))).. ( -42.80)
>DroYak_CAF1 102857 98 - 1
GGCUGUGGUGUUAUGGCCAUAACCAUAAUCGCGGCUAUAUCAGUACCCACCCUUUUUUCGCAACUUGCUGCCAAUUUGGUGGCAUGGGCGGUGGGC-U-------G
(((((((((..(((((......))))))))))))))....(((..((((((........((....(((..((.....))..)))...)))))))))-)-------) ( -37.90)
>DroAna_CAF1 97413 84 - 1
-----UCGAGUUAUGGCA--AACCAUAAUCGUUGGAAUAUCAAUGCCCACCCAUUUUUCGCAAGUUCCUUGG--------GAUAUAGGGUUAGGGCAA-------G
-----.(((.((((((..--..)))))))))............(((((((((.....((.((((...)))).--------))....))))..))))).-------. ( -25.80)
>consensus
GGCUGUGGUGUUAUGGCCAUAACCAUAAUCGCGGCAAUAUCAGUGCCCACCCUUUUUUCGCAACUUGCUGCCAAUUUGGUGGCAUGGGCGUUGGGC_G_______G
....((.(((((((((......)))))).))).))..............(((......(((....(((((((.....)))))))...)))..)))........... (-21.54 = -23.07 +   1.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:18 2006