Locus 5778

Sequence ID	2L_DroMel_CAF1
Location	16,393,989 – 16,394,176
Length	187
Max. P	0.994877

overview

Window 1

Location	16,393,989 – 16,394,106
Length	117
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	98.46
Mean single sequence MFE	-18.93
Consensus MFE	-17.19
Energy contribution	-17.03
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.71
Structure conservation index	0.91
SVM decision value	1.23
SVM RNA-class probability	0.933061
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16393989 117 + 22407834
GCAAAAUGUAUUUUCCCAUUGCAUUUUCGAUUAGUUUUUCUGAUUUGACCAUACAUAUUUGCACAAACAAUCAACAAAAUAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUAUUUGC
(((((((((((..((.............((((((.....)))))).))..)))))).))))).....(((..(((((.......((((((......))))))....)))))..))). ( -17.94)
>DroSec_CAF1 18542 117 + 1
GCAGAAUGUAUUUUCCCAUUGCAUUUUCGAUUAGUUUUUCUGAUUUGACCAUACAUAUUUGCACAAACAAUCAACAAAAUAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUAUUUGC
(((((((((((..((.............((((((.....)))))).))..)))))).))))).....(((..(((((.......((((((......))))))....)))))..))). ( -18.04)
>DroSim_CAF1 17048 117 + 1
GCAAAAUGUAUUUUCCCAUUGCAUUUUCGAUUAGUUUUUCUGAUUUGACCAUACAUAUUUGCACAAACAAUCAACAAAAUAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUAUUUGC
(((((((((((..((.............((((((.....)))))).))..)))))).))))).....(((..(((((.......((((((......))))))....)))))..))). ( -17.94)
>DroEre_CAF1 15197 117 + 1
GCAAAAUGUAUUUUCCCACUGCAUUUUCGAUUAGUUUUUCUGAUUUGACCAUACAUAUUUGCACAAACAAUCAACAAAAUAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUGUUUGC
(((((((((((..((.............((((((.....)))))).))..)))))).))))).....(((.((((((.......((((((......))))))....)))))).))). ( -20.74)
>DroYak_CAF1 18999 117 + 1
GCAAAAUGUAUUUCCCCAUUGCAUUUUCGAUUAGUUUUUCUGAUUUGACCAUACAUAUUUGCACAAACAAUCAACAAAAUAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUGUUUGC
((((((((((.........)))))..((((((((.....)))).)))).........))))).....(((.((((((.......((((((......))))))....)))))).))). ( -20.00)
>consensus
GCAAAAUGUAUUUUCCCAUUGCAUUUUCGAUUAGUUUUUCUGAUUUGACCAUACAUAUUUGCACAAACAAUCAACAAAAUAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUAUUUGC
(((((((((((...............((((((((.....)))).))))..)))))).))))).....(((..(((((.......((((((......))))))....)))))..))). (-17.19 = -17.03 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	16,394,029 – 16,394,145
Length	116
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	97.16
Mean single sequence MFE	-26.50
Consensus MFE	-24.04
Energy contribution	-23.64
Covariance contribution	-0.40
Combinations/Pair	1.06
Mean z-score	-2.07
Structure conservation index	0.91
SVM decision value	2.52
SVM RNA-class probability	0.994877
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16394029 116 - 22407834
UCGCCGCCA-AUCGACGAACGCCUAAGCAUCGAAAUUAGCGCAAAUAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUAUUUUGUUGAUUGUUUGUGCAAAUAUGUAUGGUCAAAUCA
..(((..((-(((((((((.((((((.........)))).)).............((((((......))))))......)))))))))))...(((((....))))))))....... ( -25.80)
>DroSec_CAF1 18582 116 - 1
UAGCCGCCA-AUCGACGAACGCCUAAGCACCGAAAUUAGCGCAAAUAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUAUUUUGUUGAUUGUUUGUGCAAAUAUGUAUGGUCAAAUCA
..(((..((-(((((((((.((((((.........)))).)).............((((((......))))))......)))))))))))...(((((....))))))))....... ( -25.80)
>DroSim_CAF1 17088 116 - 1
UCGCCGCCA-AUCGACGAACGCCUAAGCACCAAAAUUAGCGCAAAUAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUAUUUUGUUGAUUGUUUGUGCAAAUAUGUAUGGUCAAAUCA
..(((..((-(((((((((.((((((.........)))).)).............((((((......))))))......)))))))))))...(((((....))))))))....... ( -25.80)
>DroEre_CAF1 15237 117 - 1
UGGCCGCCAAAUCGACGAACGCCUAAGCAACGAAAUUAGCGCAAACAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUAUUUUGUUGAUUGUUUGUGCAAAUAUGUAUGGUCAAAUCA
((((((..............((....))..........(((((((((((((((((((((((......))))))..)))....)))).)))))))))).........))))))..... ( -27.50)
>DroYak_CAF1 19039 116 - 1
UAGCCGCCA-AUCGACGGACGCCUAAGCACCGAAAUUAGCGCAAACAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUAUUUUGUUGAUUGUUUGUGCAAAUAUGUAUGGUCAAAUCA
.....((((-.....(((..((....)).)))......(((((((((((((((((((((((......))))))..)))....)))).)))))))))).........))))....... ( -27.60)
>consensus
UAGCCGCCA_AUCGACGAACGCCUAAGCACCGAAAUUAGCGCAAAUAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUAUUUUGUUGAUUGUUUGUGCAAAUAUGUAUGGUCAAAUCA
.............(((.(((((....))..........(((((((((((((((((((((((......))))))..)))....)))).))))))))))......)).).)))...... (-24.04 = -23.64 +  -0.40)

alignment

secondary structure

dotplot

Window 3

Location	16,394,068 – 16,394,176
Length	108
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	92.68
Mean single sequence MFE	-34.26
Consensus MFE	-26.74
Energy contribution	-26.90
Covariance contribution	0.16
Combinations/Pair	1.12
Mean z-score	-1.70
Structure conservation index	0.78
SVM decision value	0.37
SVM RNA-class probability	0.709822
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16394068 108 + 22407834
UAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUAUUUGCGCUAAUUUCGAUGCUUAGGCGUUCGUCGAU-UGGCGGCGAGU-------GGGCGUGGU--CGCCAGUAAACAGCCUGCAU
(((((((((((......))))..))))))).....((((((((((.((((((....))).)))..)))-))))(((..((-------.((((....--)))).....)).))).))). ( -32.60)
>DroSec_CAF1 18621 108 + 1
UAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUAUUUGCGCUAAUUUCGGUGCUUAGGCGUUCGUCGAU-UGGCGGCUAGU-------GGGCGUGGU--CGCCAGUAAAUAGCCUGCAU
(((((((((((......))))..)))))))......(((((......))))).(((((........((-((((((((((.-------...).))))--))))))).....)))))... ( -33.02)
>DroSim_CAF1 17127 108 + 1
UAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUAUUUGCGCUAAUUUUGGUGCUUAGGCGUUCGUCGAU-UGGCGGCGAGU-------GGGCGUGGU--CGCCAGUAAACAGCCUGCAU
(((((((((((......))))..)))))))......((((((....)))))).(((((....((..((-(((((((.((.-------...).).))--)))))))..)).)))))... ( -33.20)
>DroEre_CAF1 15276 118 + 1
UAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUGUUUGCGCUAAUUUCGUUGCUUAGGCGUUCGUCGAUUUGGCGGCCAGUGGGCAGUGGGCGUGGUCCCGCCCGUAAAUAGCCUGCAU
.((((((((((......))))..))))))((((((((((((((..(((.(((....))).....))).))))).(((....)))...(((((......))))))))))))))...... ( -36.10)
>DroYak_CAF1 19078 108 + 1
UAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUGUUUGCGCUAAUUUCGGUGCUUAGGCGUCCGUCGAU-UGGCGGCUAGU-------GGGCGUGGU--CGCCGGUAAACAGCCUGCAU
.((((((((((......))))..))))))((((((((((((((((.((((((....))).)))..)))-)))).......-------.((((....--)))).)))))))))...... ( -36.40)
>consensus
UAAUUAAAUGCAUUCAAGCAUUUUUAAUUGUUAUUUGCGCUAAUUUCGGUGCUUAGGCGUUCGUCGAU_UGGCGGCGAGU_______GGGCGUGGU__CGCCAGUAAACAGCCUGCAU
.((((((((((......))))..))))))(((((((((((((...(((((((....)))....))))..))))...............((((......)))).)))))))))...... (-26.74 = -26.90 +   0.16)

alignment

secondary structure

dotplot

Window 4

Location	16,394,068 – 16,394,176
Length	108
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	92.68
Mean single sequence MFE	-25.12
Consensus MFE	-19.88
Energy contribution	-19.88
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.79
SVM decision value	0.10
SVM RNA-class probability	0.585315
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16394068 108 - 22407834
AUGCAGGCUGUUUACUGGCG--ACCACGCCC-------ACUCGCCGCCA-AUCGACGAACGCCUAAGCAUCGAAAUUAGCGCAAAUAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUA
.(((.(((.((.....((((--....)))).-------....)).))).-.....(((..((....)).)))........)))............((((((......))))))..... ( -23.30)
>DroSec_CAF1 18621 108 - 1
AUGCAGGCUAUUUACUGGCG--ACCACGCCC-------ACUAGCCGCCA-AUCGACGAACGCCUAAGCACCGAAAUUAGCGCAAAUAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUA
.(((.(((((......((((--....)))).-------..)))))((.(-((...((...((....))..))..))).)))))............((((((......))))))..... ( -23.20)
>DroSim_CAF1 17127 108 - 1
AUGCAGGCUGUUUACUGGCG--ACCACGCCC-------ACUCGCCGCCA-AUCGACGAACGCCUAAGCACCAAAAUUAGCGCAAAUAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUA
.(((((((........((((--....)))).-------..(((.((...-..)).)))..))))..((..........)))))............((((((......))))))..... ( -23.00)
>DroEre_CAF1 15276 118 - 1
AUGCAGGCUAUUUACGGGCGGGACCACGCCCACUGCCCACUGGCCGCCAAAUCGACGAACGCCUAAGCAACGAAAUUAGCGCAAACAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUA
.(((((((.......(((((......)))))...(((....)))................))))..((..........)))))............((((((......))))))..... ( -29.60)
>DroYak_CAF1 19078 108 - 1
AUGCAGGCUGUUUACCGGCG--ACCACGCCC-------ACUAGCCGCCA-AUCGACGGACGCCUAAGCACCGAAAUUAGCGCAAACAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUA
.(((.(((.(((....((((--....)))).-------...))).))).-.....(((..((....)).)))........)))............((((((......))))))..... ( -26.50)
>consensus
AUGCAGGCUGUUUACUGGCG__ACCACGCCC_______ACUAGCCGCCA_AUCGACGAACGCCUAAGCACCGAAAUUAGCGCAAAUAACAAUUAAAAAUGCUUGAAUGCAUUUAAUUA
.(((((((........((((......))))..............((.(.....).))...))))..((..........)))))............((((((......))))))..... (-19.88 = -19.88 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:31 2006