Locus 1552

Sequence ID	X_DroMel_CAF1
Location	4,461,985 – 4,462,202
Length	217
Max. P	0.999359

overview

Window 2

Location	4,461,985 – 4,462,099
Length	114
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	95.32
Mean single sequence MFE	-41.73
Consensus MFE	-41.55
Energy contribution	-41.00
Covariance contribution	-0.55
Combinations/Pair	1.12
Mean z-score	-3.34
Structure conservation index	1.00
SVM decision value	2.59
SVM RNA-class probability	0.995562
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4461985 114 + 22224390
UACAUAUGUAUGGGCAUAUGUACACGAAGAUCUGGAUGUGCUCAUCGCUAGAUGAAGUGCGACAGAAAGGGCAACAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCC
(((((((((....)))))))))........((((..((..((((((....)))).))..)).))))..((((((......(((((.....))))).((....))....)))))) ( -42.30)
>DroSim_CAF1 68991 114 + 1
UACAUAUGCAUGUGCAUAUGUACACAAUGAUCUGGAUGUGCUCAUCGCUAGAUGAAGUGCGACAGAAAGGGCAACAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCC
(((((((((....)))))))))........((((..((..((((((....)))).))..)).))))..((((((......(((((.....))))).((....))....)))))) ( -44.40)
>DroEre_CAF1 67206 114 + 1
UAUGUAUGUAUGUACAUAUGCACACGAAGAUCUGGAUGUGCUCAUCGCUAGAUGAAGUGCGACAGAAAGGGCAACAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCC
..(((.((((((....)))))).)))....((((..((..((((((....)))).))..)).))))..((((((......(((((.....))))).((....))....)))))) ( -38.50)
>consensus
UACAUAUGUAUGUGCAUAUGUACACGAAGAUCUGGAUGUGCUCAUCGCUAGAUGAAGUGCGACAGAAAGGGCAACAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCC
(((((((((....)))))))))........((((..((..((((((....)))).))..)).))))..((((((......(((((.....))))).((....))....)))))) (-41.55 = -41.00 +  -0.55)

alignment

secondary structure

dotplot

Window 3

Location	4,461,985 – 4,462,099
Length	114
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	95.32
Mean single sequence MFE	-35.23
Consensus MFE	-32.91
Energy contribution	-33.47
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-2.38
Structure conservation index	0.93
SVM decision value	1.23
SVM RNA-class probability	0.933724
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4461985 114 - 22224390
GGGCAAAUCCCGUUGCCAUUGGCCACGCUGGCCAUGUUUGUUGCCCUUUCUGUCGCACUUCAUCUAGCGAUGAGCACAUCCAGAUCUUCGUGUACAUAUGCCCAUACAUAUGUA
((((((....(((.((((.((....)).)))).)))....))))))..((((......((((((....))))))......))))........((((((((......)))))))) ( -33.80)
>DroSim_CAF1 68991 114 - 1
GGGCAAAUCCCGUUGCCAUUGGCCACGCUGGCCAUGUUUGUUGCCCUUUCUGUCGCACUUCAUCUAGCGAUGAGCACAUCCAGAUCAUUGUGUACAUAUGCACAUGCAUAUGUA
((((((....(((.((((.((....)).)))).)))....))))))..((.(((((..........)))))))(((((..........)))))((((((((....)))))))). ( -38.30)
>DroEre_CAF1 67206 114 - 1
GGGCAAAUCCCGUUGCCAUUGGCCACGCUGGCCAUGUUUGUUGCCCUUUCUGUCGCACUUCAUCUAGCGAUGAGCACAUCCAGAUCUUCGUGUGCAUAUGUACAUACAUACAUA
((((((....(((.((((.((....)).)))).)))....))))))..((.(((((..........)))))))((((((..........)))))).((((((......)))))) ( -33.60)
>consensus
GGGCAAAUCCCGUUGCCAUUGGCCACGCUGGCCAUGUUUGUUGCCCUUUCUGUCGCACUUCAUCUAGCGAUGAGCACAUCCAGAUCUUCGUGUACAUAUGCACAUACAUAUGUA
((((((....(((.((((.((....)).)))).)))....))))))........((((...((((.(.((((....)))))))))....))))((((((((....)))))))). (-32.91 = -33.47 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	4,462,025 – 4,462,139
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.85
Mean single sequence MFE	-34.16
Consensus MFE	-31.62
Energy contribution	-32.10
Covariance contribution	0.48
Combinations/Pair	1.03
Mean z-score	-2.19
Structure conservation index	0.93
SVM decision value	3.54
SVM RNA-class probability	0.999359
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4462025 114 + 22224390
CUCAUCGCUAGAUGA------AGUGCGACAGAAAGGGCAACAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCCAAAAAUCCAAAAUGCAUCCAGACAUAUGCAUAUGUGUAUG
.(((((....)))))------.((((.(((....((((((......(((((.....))))).((....))....))))))...........((((((........)))))).))))))). ( -34.40)
>DroSec_CAF1 63560 114 + 1
CUCAUCGCUAGAUGA------AGUGCGACAGAAAGGGCAACAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUCUGCCCAAAAAUCCAAAAUGCAUCCAGACAUAUGCGUAUGUGUAUG
.(((((....)))))------.((((.(((....(((((.......(((((.....))))).((....)).....)))))...........((((((........)))))).))))))). ( -33.30)
>DroSim_CAF1 69031 114 + 1
CUCAUCGCUAGAUGA------AGUGCGACAGAAAGGGCAACAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCCAAAAAUCCAAAACGCAUCCAGACAUAUGCAUAUGUGUAUG
.(((((....)))))------.((((.(((....((((((......(((((.....))))).((....))....)))))).............((((........))))...))))))). ( -32.70)
>DroEre_CAF1 67246 114 + 1
CUCAUCGCUAGAUGA------AGUGCGACAGAAAGGGCAACAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCCAAAAAUCCAAAAUGCAUCCAGACAUAUGCAUAUGUGUAUG
.(((((....)))))------.((((.(((....((((((......(((((.....))))).((....))....))))))...........((((((........)))))).))))))). ( -34.40)
>DroYak_CAF1 64419 118 + 1
--CAUCGCUAGAUGAUGUGCAAGUGCGACAGAAAGGGCAACAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCCGAAAAUCCAAAAUGCAUCCAGGAAAAUGCAUAUGUGUAUG
--((((....))))(((..((.(((((.......((((((......(((((.....))))).((....))....)))))).....(((............)))...))))).))..))). ( -36.00)
>consensus
CUCAUCGCUAGAUGA______AGUGCGACAGAAAGGGCAACAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCCAAAAAUCCAAAAUGCAUCCAGACAUAUGCAUAUGUGUAUG
.(((((....))))).......((((.(((....((((((......(((((.....))))).((....))....))))))...........((((((........)))))).))))))). (-31.62 = -32.10 +   0.48)

alignment

secondary structure

dotplot

Window 5

Location	4,462,059 – 4,462,179
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.21
Mean single sequence MFE	-39.42
Consensus MFE	-32.74
Energy contribution	-33.18
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-2.89
Structure conservation index	0.83
SVM decision value	3.14
SVM RNA-class probability	0.998551
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4462059 120 + 22224390
CAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCCAAAAAUCCAAAAUGCAUCCAGACAUAUGCAUAUGUGUAUGUGGGUGCUACAUACAGUGAUCACUCGUAUAGAAGGCAGAA
......(((((.....))))).((....))...((((((..............((((((..((((((((....))))))))))))))...(((((((....))).))))....)))))). ( -37.30)
>DroSec_CAF1 63594 120 + 1
CAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUCUGCCCAAAAAUCCAAAAUGCAUCCAGACAUAUGCGUAUGUGUAUGUGGGUGCUACAUACAGUGAUCACUUGUAUGAAAGGCAUGA
......(((((.....)))))(((.(...(((.....))).............((((((..((((((((....))))))))))))))..((((((((....)).))))))...).))).. ( -37.80)
>DroSim_CAF1 69065 120 + 1
CAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCCAAAAAUCCAAAACGCAUCCAGACAUAUGCAUAUGUGUAUGUGGGUGCUACAUACAGUGAUCACUCGUAUGAAAGGCAGGA
....(((((((.....)))).)))((....((((((......)))))).....((((((..((((((((....))))))))))))))..((((((((....))).)))))....)).... ( -40.50)
>DroEre_CAF1 67280 115 + 1
CAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCCAAAAAUCCAAAAUGCAUCCAGACAUAUGCAUAUGUGUAUGUGGGUGCUAUAUACAGUGGGCACUCGUGGCGCGG-----A
....(((((((.....)))).)))((.(((((...((((((............((((((..((((((((....)))))))))))))).........))))))))))).))....-----. ( -43.40)
>DroYak_CAF1 64457 115 + 1
CAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCCGAAAAUCCAAAAUGCAUCCAGGAAAAUGCAUAUGUGUAUGUGGGUGCUACAUACAGUGUGCACUCGUAGCACAG-----A
....(((((((.....)))).)))((.(((((((((......))))))..................(((((((.(((((((((...))))))))))))))))..))).))....-----. ( -38.10)
>consensus
CAAACAUGGCCAGCGUGGCCAAUGGCAACGGGAUUUGCCCAAAAAUCCAAAAUGCAUCCAGACAUAUGCAUAUGUGUAUGUGGGUGCUACAUACAGUGAUCACUCGUAUCAAAGGCA__A
......(((((.....))))).((....))((((((......)))))).....(((((((..(((((((....))))))))))))))....((((((....))).)))............ (-32.74 = -33.18 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	4,462,099 – 4,462,202
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.21
Mean single sequence MFE	-27.66
Consensus MFE	-17.42
Energy contribution	-18.66
Covariance contribution	1.24
Combinations/Pair	1.04
Mean z-score	-2.20
Structure conservation index	0.63
SVM decision value	1.82
SVM RNA-class probability	0.978853
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4462099 103 + 22224390
AAAAAUCCAAAAUGCAUCCAGACAUAUGCAUAUGUGUAUGUGGGUGCUACAUACAGUGAUCACUCGUAUAGAAGGCAGAAAAAGU-UGACAAU------------UGGAGAUUUGG----
.....(((((...((((((..((((((((....))))))))))))))...(((((((....))).))))................-......)------------)))).......---- ( -24.70)
>DroSec_CAF1 63634 103 + 1
AAAAAUCCAAAAUGCAUCCAGACAUAUGCGUAUGUGUAUGUGGGUGCUACAUACAGUGAUCACUUGUAUGAAAGGCAUGAAAAGU-UGACAAU------------UUGAGAUUUGG----
..(((((((((..((((((..((((((((....))))))))))))))..((((((((....)).))))))...............-......)------------))).)))))..---- ( -27.10)
>DroSim_CAF1 69105 103 + 1
AAAAAUCCAAAACGCAUCCAGACAUAUGCAUAUGUGUAUGUGGGUGCUACAUACAGUGAUCACUCGUAUGAAAGGCAGGAAAAGU-UGACAAU------------UUGAGAUUUGG----
..(((((((((..((((((..((((((((....))))))))))))))..((((((((....))).)))))...............-......)------------))).)))))..---- ( -28.10)
>DroEre_CAF1 67320 115 + 1
AAAAAUCCAAAAUGCAUCCAGACAUAUGCAUAUGUGUAUGUGGGUGCUAUAUACAGUGGGCACUCGUGGCGCGG-----AAAAGUGUGAUAAUGCUCCUCUUUACUUCAGUUUUGGUGCU
......(((((((((((((..((((((((....)))))))))))))).......((.(((((...((.((((..-----....)))).))..)))))))..........))))))).... ( -34.10)
>DroYak_CAF1 64497 94 + 1
GAAAAUCCAAAAUGCAUCCAGGAAAAUGCAUAUGUGUAUGUGGGUGCUACAUACAGUGUGCACUCGUAGCACAG-----ACAAGU-UGGUAAUACUGCUU--------------------
......((((.((((((........)))))).(((((.(((((((((.((((...)))))))))))))))))).-----.....)-)))...........-------------------- ( -24.30)
>consensus
AAAAAUCCAAAAUGCAUCCAGACAUAUGCAUAUGUGUAUGUGGGUGCUACAUACAGUGAUCACUCGUAUCAAAGGCA__AAAAGU_UGACAAU____________UUGAGAUUUGG____
......(((((..(((((((..(((((((....))))))))))))))....((((((....))).)))...........................................))))).... (-17.42 = -18.66 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:15 2006