Locus 2317

Sequence ID	2L_DroMel_CAF1
Location	6,286,581 – 6,286,731
Length	150
Max. P	0.998395

overview

Window 9

Location	6,286,581 – 6,286,701
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.67
Mean single sequence MFE	-19.02
Consensus MFE	-18.20
Energy contribution	-18.08
Covariance contribution	-0.12
Combinations/Pair	1.07
Mean z-score	-1.51
Structure conservation index	0.96
SVM decision value	1.08
SVM RNA-class probability	0.911280
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6286581 120 + 22407834
UUAUUUUUCAUUUAAUUUCCAAUUCCUUCGUUCGGCGCUUUUAAUGGCACUUCAUGCAAUUAAAAUGCCAAGUCAACAAUUCUUUCAGCGAACAGCUCGUAAGCUACUAAAAAUUAUUUU
............((((((...........((((((((.(((((((.(((.....))).)))))))))))..(....)............))))((((....)))).....)))))).... ( -19.10)
>DroSec_CAF1 122838 120 + 1
UUAUUUUUCAUUUAAUUUCCAAUUCCUUCGUUCGGCGCUUUUAAUGGCACUUCAUGCAAUUAAAAUGCCAAGUCAACAAUUCUUUCAGCGAACAGCUCGUAAGCUACUAAAAAUUAUUUU
............((((((...........((((((((.(((((((.(((.....))).)))))))))))..(....)............))))((((....)))).....)))))).... ( -19.10)
>DroSim_CAF1 137557 120 + 1
UUAUUUUUCAUUUAAUUUCCAAUUCCUUCGUUCGGCGCUUUUAAUGGCACUUCAUGCAAUUAAAAUGCCAAGUCAACAAUUCUUUCAGCGAACAGCUCGUAAGCUACUAAAAAUUAUUUU
............((((((...........((((((((.(((((((.(((.....))).)))))))))))..(....)............))))((((....)))).....)))))).... ( -19.10)
>DroEre_CAF1 122497 120 + 1
UUACUUUUCAUUUAAUUUCCAAUUCCUUCGUUCGGCGCUUUUAAUGGCACUUCAUGCAAUUAAAAUGCCAAGUCAACAAUUCUUUCAGCGAGCAGCUCGUAAGCUACUAAAAAUUAUUUU
............((((((...........((((((((.(((((((.(((.....))).)))))))))))..(....)............))))((((....)))).....)))))).... ( -19.10)
>DroYak_CAF1 135775 120 + 1
UUAUUUUUCAUUUAAUUUCCAAUUCCUUCGUUUGGCGCUUUUAAUGGCACUUCAUGCAAUUAAAAUGCCAAGUCAACAAUUCUUUCAGCGCACAGCUCGUAAGCUACUAAAAAUUAUUUU
............((((((...........((((((((.(((((((.(((.....))).)))))))))))))).)............(((..((.....))..))).....)))))).... ( -18.70)
>consensus
UUAUUUUUCAUUUAAUUUCCAAUUCCUUCGUUCGGCGCUUUUAAUGGCACUUCAUGCAAUUAAAAUGCCAAGUCAACAAUUCUUUCAGCGAACAGCUCGUAAGCUACUAAAAAUUAUUUU
............((((((...........((((((((.(((((((.(((.....))).)))))))))))..(....)............))))((((....)))).....)))))).... (-18.20 = -18.08 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	6,286,581 – 6,286,701
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.67
Mean single sequence MFE	-27.44
Consensus MFE	-26.00
Energy contribution	-26.24
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.32
Structure conservation index	0.95
SVM decision value	3.07
SVM RNA-class probability	0.998340
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6286581 120 - 22407834
AAAAUAAUUUUUAGUAGCUUACGAGCUGUUCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAAAAGCGCCGAACGAAGGAAUUGGAAAUUAAAUGAAAAAUAA
....(((((((((((..(((.(((((.((((.......)))).)))...(((((.(((((((.((((...)))).)))))))..))))).)))))..)))))))))))............ ( -27.30)
>DroSec_CAF1 122838 120 - 1
AAAAUAAUUUUUAGUAGCUUACGAGCUGUUCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAAAAGCGCCGAACGAAGGAAUUGGAAAUUAAAUGAAAAAUAA
....(((((((((((..(((.(((((.((((.......)))).)))...(((((.(((((((.((((...)))).)))))))..))))).)))))..)))))))))))............ ( -27.30)
>DroSim_CAF1 137557 120 - 1
AAAAUAAUUUUUAGUAGCUUACGAGCUGUUCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAAAAGCGCCGAACGAAGGAAUUGGAAAUUAAAUGAAAAAUAA
....(((((((((((..(((.(((((.((((.......)))).)))...(((((.(((((((.((((...)))).)))))))..))))).)))))..)))))))))))............ ( -27.30)
>DroEre_CAF1 122497 120 - 1
AAAAUAAUUUUUAGUAGCUUACGAGCUGCUCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAAAAGCGCCGAACGAAGGAAUUGGAAAUUAAAUGAAAAGUAA
..(((((((((((((((((....)))))))......)))))))))).(((((((((((((......)))))))))..........((((.(....)..))))............)))).. ( -27.10)
>DroYak_CAF1 135775 120 - 1
AAAAUAAUUUUUAGUAGCUUACGAGCUGUGCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAAAAGCGCCAAACGAAGGAAUUGGAAAUUAAAUGAAAAAUAA
....(((((((((((..(((.((...((.(((((..........((((..((((((((((......)))))))))))))).)))))))..)))))..)))))))))))............ ( -28.20)
>consensus
AAAAUAAUUUUUAGUAGCUUACGAGCUGUUCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAAAAGCGCCGAACGAAGGAAUUGGAAAUUAAAUGAAAAAUAA
....(((((((((((..(((.(((((.((((.......)))).)))...(((((.(((((((.((((...)))).)))))))..))))).)))))..)))))))))))............ (-26.00 = -26.24 +   0.24)

alignment

secondary structure

dotplot

Window 1

Location	6,286,621 – 6,286,731
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.88
Mean single sequence MFE	-29.48
Consensus MFE	-27.36
Energy contribution	-27.56
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.93
SVM decision value	3.09
SVM RNA-class probability	0.998395
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6286621 110 - 22407834
GCG--AGA--------GAGUCGUCUUUAUGACAAUCGUAAAAAAUAAUUUUUAGUAGCUUACGAGCUGUUCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAA
...--...--------((((((((.....)))..........((((((((((..((((..((.....))..)))).)))))))))))))))(((((((((......)))))))))..... ( -28.60)
>DroSec_CAF1 122878 112 - 1
GCGCGAGA--------GAGUCGUCUUUAUGACAAUCGUAAAAAAUAAUUUUUAGUAGCUUACGAGCUGUUCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAA
.(....).--------((((((((.....)))..........((((((((((..((((..((.....))..)))).)))))))))))))))(((((((((......)))))))))..... ( -29.00)
>DroSim_CAF1 137597 112 - 1
GCGAGAGA--------GAGUCGUCUUUAUGACAAUCGUAAAAAAUAAUUUUUAGUAGCUUACGAGCUGUUCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAA
........--------((((((((.....)))..........((((((((((..((((..((.....))..)))).)))))))))))))))(((((((((......)))))))))..... ( -28.60)
>DroEre_CAF1 122537 110 - 1
GCGAGAG----------AGUCGUCUUUAUGACAAUCGUAAAAAAUAAUUUUUAGUAGCUUACGAGCUGCUCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAA
......(----------(((((((.....)))..........(((((((((((((((((....)))))))......)))))))))))))))(((((((((......)))))))))..... ( -31.40)
>DroYak_CAF1 135815 120 - 1
GCGAGAGAGGGGGGCAGAGUCGUCUUUAUGACAAUCGUAAAAAAUAAUUUUUAGUAGCUUACGAGCUGUGCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAA
((...........)).((((((((.....)))..........((((((((((..((((.(((.....))).)))).)))))))))))))))(((((((((......)))))))))..... ( -29.80)
>consensus
GCGAGAGA________GAGUCGUCUUUAUGACAAUCGUAAAAAAUAAUUUUUAGUAGCUUACGAGCUGUUCGCUGAAAGAAUUGUUGACUUGGCAUUUUAAUUGCAUGAAGUGCCAUUAA
................((((((((.....)))..........(((((((((((((((((....))))....)))))..)))))))))))))(((((((((......)))))))))..... (-27.36 = -27.56 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:01 2006