Locus 70

Sequence ID	4_DroMel_CAF1
Location	549,918 – 550,107
Length	189
Max. P	0.995631

overview

Window 0

Location	549,918 – 550,030
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	71.19
Mean single sequence MFE	-31.58
Consensus MFE	-10.94
Energy contribution	-12.22
Covariance contribution	1.28
Combinations/Pair	1.17
Mean z-score	-2.19
Structure conservation index	0.35
SVM decision value	1.68
SVM RNA-class probability	0.971566
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 549918 112 - 1281640
GCAGAUGAUGCCGCAGCAUAGCUGGCAUCCGUUGUGGCAUCAUUGGUUGUGGUUCUAGCCAAAUUUAGGCCAGGUGCGAGAGAAACAUCUG--------AAAACAUAACACCUUAAUAAG
...((((((((((((((.............)))))))))))))).((((((......(((.......)))(((((((....)...))))))--------....))))))........... ( -36.92)
>DroPse_CAF1 3410 109 - 1
GC---UGUUGCUGCGGCAAAGCCGACCUCCGACGAUCCACCAACUGGUGUGUUUGUUGCCAUAUUGAAGCCAGCUUCAAAAAUGAUAUCUG--------AAAUAAAGAUCCAAUCGUAAA
((---((..(((.((((...)))).....((((((.(((((....)))).).)))))).........))))))).......(((((((((.--------......))))...)))))... ( -26.40)
>DroSim_CAF1 1604 109 - 1
GCAGAUGAUGCCGCAGCAUAGCUGGCAUCCGUU---GCAUCAUUGGUUGCGGUUCUAGCCAAAUUUAGGCCAGAUGCGAAAGAAACAUCUG--------AAAAUAAAACACCUCAAUAAA
((((..((((((((......)).))))))..))---)).......((((.(((....(((.......)))(((((((....)...))))))--------..........))).))))... ( -33.10)
>DroEre_CAF1 3026 120 - 1
GCAGAUGAUGCCUCAGCAUAGCUGGCAUCCGACGUGGCAUCAUUGGUUGUGGCUCUAGCCAAAUUAAGGCCAGAUGCAAAAGAAACAUCUGCAAAAAAAAAAAAAAAACACCUUAAUGAG
(((((((......((((...))))(((((.....((((....((((((.((((....)))))))))).)))))))))........)))))))............................ ( -35.10)
>DroPer_CAF1 5032 109 - 1
GC---UGUUGCUGCGGCAAAGCCGACCUCCGACGAUCCACCAACUGGUGUGUUUGUUGCCAUAUUGAAGCCAGCUUCAAAAAUGAUAUCUG--------AAAUAAAGAUCCAAUCGUAAA
((---((..(((.((((...)))).....((((((.(((((....)))).).)))))).........))))))).......(((((((((.--------......))))...)))))... ( -26.40)
>consensus
GCAGAUGAUGCCGCAGCAUAGCUGGCAUCCGACGAGGCAUCAUUGGUUGUGGUUCUAGCCAAAUUGAGGCCAGAUGCAAAAGAAACAUCUG________AAAAAAAAACACCUUAAUAAA
...((((((((..((((...))))............))))))))(((..........(((.......)))((((((.........))))))..................)))........ (-10.94 = -12.22 +   1.28)

alignment

secondary structure

dotplot

Window 1

Location	549,950 – 550,067
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.39
Mean single sequence MFE	-40.49
Consensus MFE	-18.90
Energy contribution	-17.54
Covariance contribution	-1.36
Combinations/Pair	1.30
Mean z-score	-2.26
Structure conservation index	0.47
SVM decision value	1.80
SVM RNA-class probability	0.977670
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 549950 117 + 1281640
CUCGCACCUGGCCUAAAUUUGGCUAGAACCACAACCAAUGAUGCCACAACGGAUGCCAGCUAUGCUGCGGCAUCAUCUGCGGC---AGUUCCUGCCAUUCCGGAUGUCAGUAUGUUUUCA
...(((.(((((.......((((..((((..((.....)).((((.((...((((((.((......))))))))...)).)))---)))))..))))........)))))..)))..... ( -35.96)
>DroPse_CAF1 3442 114 + 1
UUUGAAGCUGGCUUCAAUAUGGCAACAAACACACCAGUUGGUGGAUCGUCGGAGGUCGGCUUUGCCGCAGCAACA---GCGGG---AUCCUCCGCCGCUGCAGAUGGCAAUAUAUUAUCU
...((((((((((((....((....))....((((....))))........))))))))))))((((((((....---(((((---....))))).)))))....)))............ ( -43.40)
>DroSim_CAF1 1636 114 + 1
UUCGCAUCUGGCCUAAAUUUGGCUAGAACCGCAACCAAUGAUGC---AACGGAUGCCAGCUAUGCUGCGGCAUCAUCUGCGGC---AGCUCCUGCCAUUCCGGAUGUCAGUAUGUUUUCA
...((.(((((((.......)))))))...(((.((......((---(...((((((.((......))))))))...)))(((---((...))))).....)).)))..))......... ( -39.10)
>DroEre_CAF1 3066 120 + 1
UUUGCAUCUGGCCUUAAUUUGGCUAGAGCCACAACCAAUGAUGCCACGUCGGAUGCCAGCUAUGCUGAGGCAUCAUCUGCGGCUGGAGCCCCUGCCAUUCCGGAUGUCAAUAUGUUUUCA
.((((((((((.........((((..((((.((....((((((((..((.....))((((...)))).)))))))).)).))))..)))).........))))))).))).......... ( -40.57)
>DroPer_CAF1 5064 114 + 1
UUUGAAGCUGGCUUCAAUAUGGCAACAAACACACCAGUUGGUGGAUCGUCGGAGGUCGGCUUUGCCGCAGCAACA---GCGGG---AUCCUCCGCCGCUGCAGAUGGCAAUAUAUUAUCU
...((((((((((((....((....))....((((....))))........))))))))))))((((((((....---(((((---....))))).)))))....)))............ ( -43.40)
>consensus
UUUGCAGCUGGCCUAAAUUUGGCUAGAACCACAACCAAUGAUGCAACGUCGGAUGCCAGCUAUGCUGCGGCAUCAUCUGCGGC___AGCCCCUGCCAUUCCGGAUGUCAAUAUGUUUUCA
.......((((((.......)))................((((........(((((((((...))))..)))))....((((.........)))))))).)))................. (-18.90 = -17.54 +  -1.36)

alignment

secondary structure

dotplot

Window 2

Location	549,950 – 550,067
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.39
Mean single sequence MFE	-42.64
Consensus MFE	-21.52
Energy contribution	-20.60
Covariance contribution	-0.92
Combinations/Pair	1.33
Mean z-score	-2.52
Structure conservation index	0.50
SVM decision value	2.60
SVM RNA-class probability	0.995631
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 549950 117 - 1281640
UGAAAACAUACUGACAUCCGGAAUGGCAGGAACU---GCCGCAGAUGAUGCCGCAGCAUAGCUGGCAUCCGUUGUGGCAUCAUUGGUUGUGGUUCUAGCCAAAUUUAGGCCAGGUGCGAG
...........((.((((.((..((((.(((((.---.(.((.((((((((((((((.............)))))))))))))).)).)..))))).))))........)).)))))).. ( -44.82)
>DroPse_CAF1 3442 114 - 1
AGAUAAUAUAUUGCCAUCUGCAGCGGCGGAGGAU---CCCGC---UGUUGCUGCGGCAAAGCCGACCUCCGACGAUCCACCAACUGGUGUGUUUGUUGCCAUAUUGAAGCCAGCUUCAAA
..........(((((....((((((((((.....---.))))---))))))...)))))..........((((((.(((((....)))).).)))))).....((((((....)))))). ( -42.00)
>DroSim_CAF1 1636 114 - 1
UGAAAACAUACUGACAUCCGGAAUGGCAGGAGCU---GCCGCAGAUGAUGCCGCAGCAUAGCUGGCAUCCGUU---GCAUCAUUGGUUGCGGUUCUAGCCAAAUUUAGGCCAGAUGCGAA
...........((.((((.((..((((.((((((---((.((.((((((((.(((((...)))((...)))).---)))))))).)).)))))))).))))........)).)))))).. ( -39.20)
>DroEre_CAF1 3066 120 - 1
UGAAAACAUAUUGACAUCCGGAAUGGCAGGGGCUCCAGCCGCAGAUGAUGCCUCAGCAUAGCUGGCAUCCGACGUGGCAUCAUUGGUUGUGGCUCUAGCCAAAUUAAGGCCAGAUGCAAA
..........(((.((((.((..((((.(((((..(((((...(((((((((.((((...))))((.......))))))))))))))))..))))).))))........)).))))))). ( -45.20)
>DroPer_CAF1 5064 114 - 1
AGAUAAUAUAUUGCCAUCUGCAGCGGCGGAGGAU---CCCGC---UGUUGCUGCGGCAAAGCCGACCUCCGACGAUCCACCAACUGGUGUGUUUGUUGCCAUAUUGAAGCCAGCUUCAAA
..........(((((....((((((((((.....---.))))---))))))...)))))..........((((((.(((((....)))).).)))))).....((((((....)))))). ( -42.00)
>consensus
UGAAAACAUAUUGACAUCCGGAAUGGCAGGGGCU___GCCGCAGAUGAUGCCGCAGCAUAGCUGGCAUCCGACGAGGCAUCAUUGGUUGUGGUUCUAGCCAAAUUGAGGCCAGAUGCAAA
..........(((....((.(((((((.((((((...((((...(((((((..((((...))))............)))))))))))...)))))).))))..))).)).)))....... (-21.52 = -20.60 +  -0.92)

alignment

secondary structure

dotplot

Window 3

Location	549,990 – 550,107
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.27
Mean single sequence MFE	-41.96
Consensus MFE	-17.26
Energy contribution	-18.86
Covariance contribution	1.60
Combinations/Pair	1.21
Mean z-score	-1.92
Structure conservation index	0.41
SVM decision value	0.23
SVM RNA-class probability	0.642347
Prediction	RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 549990 117 - 1281640
UCUUAUCGCAAGAUGUUGCGCAACUUGAGGGAGAUGUUGGUGAAAACAUACUGACAUCCGGAAUGGCAGGAACU---GCCGCAGAUGAUGCCGCAGCAUAGCUGGCAUCCGUUGUGGCAU
...((((....))))((((.((.((....)).(((((..(((......)))..))))).....))))))....(---(((((((..((((((((......)).))))))..)))))))). ( -41.40)
>DroPse_CAF1 3482 114 - 1
UCUUGCCACAAGAUGUCGAGCAACUAGAGGUCGACUUUGGAGAUAAUAUAUUGCCAUCUGCAGCGGCGGAGGAU---CCCGC---UGUUGCUGCGGCAAAGCCGACCUCCGACGAUCCAC
(((((...)))))(((((........(((((((.((((((..(((...)))..))..((((((((((((.((..---.)).)---))))))))))).)))).))))))))))))...... ( -42.50)
>DroSim_CAF1 1676 114 - 1
UCUUAUCGCAAGAUGUUGCGCAACUUGAGGGAGAUGUUGGUGAAAACAUACUGACAUCCGGAAUGGCAGGAGCU---GCCGCAGAUGAUGCCGCAGCAUAGCUGGCAUCCGUU---GCAU
...((((....))))....(((((......(.(((((..(((......)))..))))))(((.((.(((..(((---((.(((.....))).)))))....))).))))))))---)).. ( -44.00)
>DroEre_CAF1 3106 120 - 1
UCUUGUCGCAAGAUGUUGCGCAACUUGAGGGAGAUGUUGGUGAAAACAUAUUGACAUCCGGAAUGGCAGGGGCUCCAGCCGCAGAUGAUGCCUCAGCAUAGCUGGCAUCCGACGUGGCAU
((((((((((((.((.....)).))))...(.(((((..(((......)))..))))))....))))))))......(((((....((((((..(((...)))))))))....))))).. ( -39.40)
>DroPer_CAF1 5104 114 - 1
UCUUGCCACAAGAUGUCGAGCAACUAGAGGUCGACUUUGGAGAUAAUAUAUUGCCAUCUGCAGCGGCGGAGGAU---CCCGC---UGUUGCUGCGGCAAAGCCGACCUCCGACGAUCCAC
(((((...)))))(((((........(((((((.((((((..(((...)))..))..((((((((((((.((..---.)).)---))))))))))).)))).))))))))))))...... ( -42.50)
>consensus
UCUUGUCGCAAGAUGUUGCGCAACUUGAGGGAGAUGUUGGUGAAAACAUAUUGACAUCCGGAAUGGCAGGGGCU___GCCGCAGAUGAUGCCGCAGCAUAGCUGGCAUCCGACGAGGCAU
(((((((.((((.((.....)).)))).....((((((((((......))))))))))......))))))).........((...(((((...((((...)))).....)))))..)).. (-17.26 = -18.86 +   1.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:33:31 2006