Locus 5463

Sequence ID	3R_DroMel_CAF1
Location	14,444,851 – 14,445,147
Length	296
Max. P	0.982965

overview

Window 0

Location	14,444,851 – 14,444,971
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.22
Mean single sequence MFE	-32.52
Consensus MFE	-23.36
Energy contribution	-22.40
Covariance contribution	-0.96
Combinations/Pair	1.25
Mean z-score	-2.09
Structure conservation index	0.72
SVM decision value	0.34
SVM RNA-class probability	0.695823
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14444851 120 - 27905053
GAAUUCCAAGCGCUGCAUCCAUGUAAAAAAUACCUGGAGCGGGCCGAGUUCGUCCGAAAUAUUCCAAAAUGCAUAGCGCACGGCAGAGGACGGGAAAGAAAUGAACCCCAUUCCUGAAAA
.....((..((((((((((((.(((.....))).)))).(((((.(....)))))).............)))..)))))..))(((.(((.(((..(....)....))).)))))).... ( -31.30)
>DroSec_CAF1 2003 118 - 1
GAAUUCCAAGCGCUGCAUCCGUGUAAAAAAUACCUGGAGCGGGUCGAGUUCGUCCGAAAUAUUCCAAAAUGCAAAGCGCACGGCAGAGGAUGAGAAAGAAAUGAAU--CAUUCCUGCAAA
.........((((((((((((.(((.....))).)))).((((.((....)))))).............)))..)))))...((((.((((((...(....)...)--)))))))))... ( -35.60)
>DroSim_CAF1 2072 118 - 1
GAAUUCCAAGCGCUGCAUCCAUGUAAAAAAUACCUGGAGCGGGUCGCGUUCGUCCGAAAUAUUCCAAAAUGCAUAGCGCACGGCAGAGGAUGAGAAAGAAAUGAAU--CAUUCCUGCAAA
.........(((((((.((((.(((.....))).))))))(((.....(((....)))....))).........)))))...((((.((((((...(....)...)--)))))))))... ( -34.80)
>DroEre_CAF1 1973 116 - 1
GAAUUCCAAGUGCUGCAUCCAUGUAAAAAAUACCUGGAGCGGGCAGAGUUCGUCCGAAAUAUUCCGAACUGCAUAA--CACGGCAGUGGAUGAGAAAGAAAUGAAC--CAUCCCUGAAAA
.........(((((((.((((.(((.....))).))))))))(((..(((((............))))))))....--)))..(((.(((((....(....)....--)))))))).... ( -29.70)
>DroYak_CAF1 2105 116 - 1
GAAUUCCAAGUGCUGCAUCUAUGUAAAAAAUACCUGGAGCGGACAGAGUUCGUCCGAAAUAUUCCAAACUGCAAGA--CACGGCGGAGGAUGGGAAAGAAAUGAAC--CAUCCCUGAAAA
.........((((((((((((.(((.....))).)))).(((((.......))))).............))).)).--)))..(((.((((((...(....)...)--)))))))).... ( -31.20)
>consensus
GAAUUCCAAGCGCUGCAUCCAUGUAAAAAAUACCUGGAGCGGGCCGAGUUCGUCCGAAAUAUUCCAAAAUGCAUAGCGCACGGCAGAGGAUGAGAAAGAAAUGAAC__CAUUCCUGAAAA
((((((...((.((((.((((.(((.....))).)))))))))).))))))................................(((.(((((....(....)......)))))))).... (-23.36 = -22.40 +  -0.96)

alignment

secondary structure

dotplot

Window 1

Location	14,444,931 – 14,445,051
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.20
Mean single sequence MFE	-36.76
Consensus MFE	-31.60
Energy contribution	-31.68
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.24
Structure conservation index	0.86
SVM decision value	0.08
SVM RNA-class probability	0.571471
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14444931 120 - 27905053
CAUCGGGGGAGCAGCACAGCAGAAAGGAAUGUGUGCAUUUGUCUGGCACUGACUUCGUGGGAGAUUGGGCAGAUGUUUUGGAAUUCCAAGCGCUGCAUCCAUGUAAAAAAUACCUGGAGC
..(((((((((((((.(....)...(((((....(((((((((..((.((.((...)).)).).)..)))))))))......)))))....))))).))).(((.....))))))))... ( -36.30)
>DroSec_CAF1 2081 117 - 1
CAACGGUGGAG---CGCAGCAGCAAGGAAUGUGUGCAUUUGUCUGGCACUGACUUCGUGGGAGAUUGGGCAGAUGUUUUGGAAUUCCAAGCGCUGCAUCCGUGUAAAAAAUACCUGGAGC
...(((.(((.---.(((((.((..(((((....(((((((((..((.((.((...)).)).).)..)))))))))......)))))..))))))).)))((((.....))))))).... ( -39.00)
>DroSim_CAF1 2150 117 - 1
CAACGGGGGAG---CGCAGCAGCAAGGAAUGUGUGCAUUUGUCUGGCACUGACUUCGUGGGAGAUUGGGCAGAUGUUUUGGAAUUCCAAGCGCUGCAUCCAUGUAAAAAAUACCUGGAGC
...(((((((.---.(((((.((..(((((....(((((((((..((.((.((...)).)).).)..)))))))))......)))))..))))))).))).(((.....))))))).... ( -40.20)
>DroEre_CAF1 2049 112 - 1
C---GGGGGA-----GCAGCAGAAAGGAAUGUGUGCAUUUGUCUGGCACUGACUUCGUGGGAGAUUGGGCAGAUGUUUCGGAAUUCCAAGUGCUGCAUCCAUGUAAAAAAUACCUGGAGC
(---((((((-----((((((....(((((.((.(((((((((..((.((.((...)).)).).)..)))))))))..))..)))))...)))))).))).(((.....))))))).... ( -37.60)
>DroYak_CAF1 2181 112 - 1
C---GGGGGA-----ACAGCAGAAAGGAAUGUGUGCAUUUGUCUGGCACUGACUUCGUGGGAGAUUGGGCAGAUGUUUCGGAAUUCCAAGUGCUGCAUCUAUGUAAAAAAUACCUGGAGC
(---((((((-----.(((((....(((((.((.(((((((((..((.((.((...)).)).).)..)))))))))..))..)))))...)))))..))).(((.....))))))).... ( -30.70)
>consensus
CA_CGGGGGAG___CGCAGCAGAAAGGAAUGUGUGCAUUUGUCUGGCACUGACUUCGUGGGAGAUUGGGCAGAUGUUUUGGAAUUCCAAGCGCUGCAUCCAUGUAAAAAAUACCUGGAGC
...............(((((.....(((((....(((((((((..((.((.((...)).)).).)..)))))))))......)))))....))))).((((.(((.....))).)))).. (-31.60 = -31.68 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	14,445,011 – 14,445,131
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.71
Mean single sequence MFE	-40.94
Consensus MFE	-34.32
Energy contribution	-34.36
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-2.08
Structure conservation index	0.84
SVM decision value	1.93
SVM RNA-class probability	0.982965
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14445011 120 - 27905053
UUGGAGCCGUGGGGCAAAGUUGAGGUAAACGUGCUCCACAUCGAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAUCAUCGGGGGAGCAGCACAGCAGAAAGGAAUGUGUGCAUUU
........((((((((..(((......))).))))))))...(((((((((.(((((((.(((....(((..(..(((......)))..)))).))).)))......))))))))))))) ( -41.90)
>DroSec_CAF1 2161 117 - 1
UUGGAGCCGUGGGGCAAAGUUGAGGUAAACGUGCUCCACAUCGAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAUCAACGGUGGAG---CGCAGCAGCAAGGAAUGUGUGCAUUU
........((((((((..(((......))).))))))))...(((((((((((((((.......)))))).(((((((((.....)))).(---(......))..))))).))))))))) ( -38.80)
>DroSim_CAF1 2230 117 - 1
UUGGAGCCGUGGGGCAAAGUUGAGGUAAACGUGCUCCACAUCGAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAUCAACGGGGGAG---CGCAGCAGCAAGGAAUGUGUGCAUUU
........((((((((..(((......))).))))))))...(((((((((.(((((....((....(((..(..(((......)))..).---.)))....))..)))))))))))))) ( -41.90)
>DroEre_CAF1 2129 112 - 1
UUGGAGCCGUGGGCCAAAGUUGAGGUAAACGUGCUCCACAUCGAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAUC---GGGGGA-----GCAGCAGAAAGGAAUGUGUGCAUUU
.(((((((((..(((........)))..))).))))))....(((((((((.((((((((.......)))..((((((...---.)))))-----)..........)))))))))))))) ( -41.10)
>DroYak_CAF1 2261 112 - 1
UUGGAGCCGUGGGCCACAGUUGAGGUAAACGUGCUCCACAUCAAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAUC---GGGGGA-----ACAGCAGAAAGGAAUGUGUGCAUUU
.(((((((((..(((........)))..))).))))))....(((((((((.((((((((.......)))..((((((...---.)))))-----)..........)))))))))))))) ( -41.00)
>consensus
UUGGAGCCGUGGGGCAAAGUUGAGGUAAACGUGCUCCACAUCGAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAUCA_CGGGGGAG___CGCAGCAGAAAGGAAUGUGUGCAUUU
.(((((((((..(.(........).)..))).))))))....(((((((((.((((((((.......)))..((((((......))))))................)))))))))))))) (-34.32 = -34.36 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	14,445,051 – 14,445,147
Length	96
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.61
Mean single sequence MFE	-38.92
Consensus MFE	-28.14
Energy contribution	-30.02
Covariance contribution	1.88
Combinations/Pair	1.03
Mean z-score	-1.95
Structure conservation index	0.72
SVM decision value	0.29
SVM RNA-class probability	0.672116
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14445051 96 - 27905053
GAGUAGG------------------------GAUUCAUAGUUGGAGCCGUGGGGCAAAGUUGAGGUAAACGUGCUCCACAUCGAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAU
.....((------------------------((((((....))))(((((((((((..(((......))).))))))))..((....)).)))..(((((.......)))))..)))).. ( -31.10)
>DroSec_CAF1 2198 120 - 1
GAGUAGGGAGUGCGGACGGAGGGAAUACGGGGAUUCAUAGUUGGAGCCGUGGGGCAAAGUUGAGGUAAACGUGCUCCACAUCGAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAU
.....(((((((((..(((...........((.((((....)))).))((((((((..(((......))).)))))))).)))..))))).((((((.......))))))....)))).. ( -41.10)
>DroSim_CAF1 2267 120 - 1
GAGUAGGGAGUGCGGACGGAGGGAAUACGGGGAUUCAUAGUUGGAGCCGUGGGGCAAAGUUGAGGUAAACGUGCUCCACAUCGAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAU
.....(((((((((..(((...........((.((((....)))).))((((((((..(((......))).)))))))).)))..))))).((((((.......))))))....)))).. ( -41.10)
>DroEre_CAF1 2161 118 - 1
GAGUAGGGAGUGCGGACGGAGGGAAUACG--GAUUCAUAGUUGGAGCCGUGGGCCAAAGUUGAGGUAAACGUGCUCCACAUCGAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAU
.....(((((((((..((..(.((((...--.)))).....(((((((((..(((........)))..))).)))))))..))..))))).((((((.......))))))....)))).. ( -41.40)
>DroYak_CAF1 2293 118 - 1
GAGAAGGGAGUGCGGGCGGAGGGAAAACG--GAUUCAUAGUUGGAGCCGUGGGCCACAGUUGAGGUAAACGUGCUCCACAUCAAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAU
.....(((((((((.((.....(((....--..)))...((.((((((((..(((........)))..))).))))))).....)).))))((((((.......))))))...))))).. ( -39.90)
>consensus
GAGUAGGGAGUGCGGACGGAGGGAAUACG__GAUUCAUAGUUGGAGCCGUGGGGCAAAGUUGAGGUAAACGUGCUCCACAUCGAGUGCGCGGCAUUUGCAGUGAAAAUGCAAUUUCCCAU
.....(((((.(((.((................((((....))))...((((((((..(((......))).)))))))).....)).))).((((((.......))))))...))))).. (-28.14 = -30.02 +   1.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:22 2006