Locus 168

Sequence ID	2R_DroMel_CAF1
Location	1,427,860 – 1,428,060
Length	200
Max. P	0.978774

overview

Window 5

Location	1,427,860 – 1,427,980
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-39.48
Consensus MFE	-35.88
Energy contribution	-36.68
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.91
SVM decision value	0.79
SVM RNA-class probability	0.850877
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1427860 120 + 20766785
CAAUGGCAUUACUUCACCCACUCGCCUCAUGUGGCUGCUCGUUAUUAUUAGCAUAAUUACAGGCGCAUUAGCGUGCCGGGUUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUG
...............((((....(((......)))((((.((....)).))))........(((((......)))))))))..(((((((((((((..........))))))).)))))) ( -40.50)
>DroSec_CAF1 46314 120 + 1
CAAUGGCAUUACUUCACCCACUCGCCUCAUGUGGCUGCUCGUUAUUAUUAGCAUAAUUACAGGCGCAUUAGCGUGCCGGGUUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUG
...............((((....(((......)))((((.((....)).))))........(((((......)))))))))..(((((((((((((..........))))))).)))))) ( -40.50)
>DroSim_CAF1 51364 120 + 1
CAAUGGCAUUACUUCACCCACUCGCCUCAUGUGGCUGCUCGUUAUUAUUAGCAUAAUUACAGGCGCAUUAGCGUGCCGGGUUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUG
...............((((....(((......)))((((.((....)).))))........(((((......)))))))))..(((((((((((((..........))))))).)))))) ( -40.50)
>DroEre_CAF1 44446 120 + 1
CAAUGGCAUUACUUCACCCACUCGCCUCAUGUGGCUGCUCGUUAUUAUUAGCAUAAUUACAGGCGCAUUAGCGUGCCAGGUUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUG
...((((((..............(((......))).((..((.(((((....))))).))..))((....)))))))).....(((((((((((((..........))))))).)))))) ( -38.10)
>DroYak_CAF1 48966 120 + 1
CAAUGGCAUUACUUCACCCACUCGACUCAUGUGGCUGCUCGUUAUUAUUAGCAUAAUUACAGGCGCAUUAACGUGCCGGGUUUCAGGGGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUA
....(((.........(((.((.(((((.(((((.((((.((....)).))))...)))))(((((......))))))))))..)))))(((((((..........)))))))..))).. ( -37.80)
>consensus
CAAUGGCAUUACUUCACCCACUCGCCUCAUGUGGCUGCUCGUUAUUAUUAGCAUAAUUACAGGCGCAUUAGCGUGCCGGGUUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUG
...............((((....(((......)))((((.((....)).))))........(((((......)))))))))..(((((((((((((..........))))))).)))))) (-35.88 = -36.68 +   0.80)

alignment

secondary structure

dotplot

Window 6

Location	1,427,900 – 1,428,020
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.50
Mean single sequence MFE	-40.20
Consensus MFE	-35.46
Energy contribution	-35.70
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.82
Structure conservation index	0.88
SVM decision value	1.69
SVM RNA-class probability	0.972185
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1427900 120 + 20766785
GUUAUUAUUAGCAUAAUUACAGGCGCAUUAGCGUGCCGGGUUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUGAUUAUGACAGGGCCUAAAAGCGAGACGCAUCCACAAUGCA
..........((((.......(((((......)))))((((.((((((((((((((..........))))))).)))))))..................(((...)))))))...)))). ( -39.80)
>DroSec_CAF1 46354 120 + 1
GUUAUUAUUAGCAUAAUUACAGGCGCAUUAGCGUGCCGGGUUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUGAUUAUGAUAGGGCCUAAAAGCGGGACGCAUCCACAAUGCA
..........((((.......(((((......)))))((((.((((((((((((((..........))))))).)))))))........(.((((......))).).)))))...)))). ( -41.30)
>DroSim_CAF1 51404 120 + 1
GUUAUUAUUAGCAUAAUUACAGGCGCAUUAGCGUGCCGGGUUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUGAUUAUGAUAGGGCCUAAAAGCGGGACGCAUCCACAAUGCA
..........((((.......(((((......)))))((((.((((((((((((((..........))))))).)))))))........(.((((......))).).)))))...)))). ( -41.30)
>DroEre_CAF1 44486 120 + 1
GUUAUUAUUAGCAUAAUUACAGGCGCAUUAGCGUGCCAGGUUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUGAUUAUGAUAGGGCCUAAAAGCGAGACGCAUCCACAAUGCA
..........((((.......(((((......)))))(((((((((((((((((((..........))))))).))))))).........)))))....(((...))).......)))). ( -38.70)
>DroYak_CAF1 49006 120 + 1
GUUAUUAUUAGCAUAAUUACAGGCGCAUUAACGUGCCGGGUUUCAGGGGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUAAUUAUGAUAGGGCCUUAAAACGAGGCGCAUCUACAAUGCA
.......(((.(((((((...(((((......)))))((((.((...(((..(((.....)))....)))..)).))))))))))).))).(((((.....)))))((((.....)))). ( -39.90)
>consensus
GUUAUUAUUAGCAUAAUUACAGGCGCAUUAGCGUGCCGGGUUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUGAUUAUGAUAGGGCCUAAAAGCGAGACGCAUCCACAAUGCA
((((....)))).........(((((......)))))(((((((((((((((((((..........))))))).))))))).........)))))...........((((.....)))). (-35.46 = -35.70 +   0.24)

alignment

secondary structure

dotplot

Window 7

Location	1,427,940 – 1,428,060
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.08
Mean single sequence MFE	-43.82
Consensus MFE	-36.86
Energy contribution	-37.14
Covariance contribution	0.28
Combinations/Pair	1.09
Mean z-score	-2.01
Structure conservation index	0.84
SVM decision value	1.82
SVM RNA-class probability	0.978774
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1427940 120 + 20766785
UUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUGAUUAUGACAGGGCCUAAAAGCGAGACGCAUCCACAAUGCACCUCCUGCAGUGCCGCUUAAGCGCUUAAAGUUGCGCAGUU
..((((((((((((((..........))))))).)))))))....(((..(((((...((.(((..((((.....))))..)))))..)).)))......((((........)))).))) ( -42.90)
>DroSec_CAF1 46394 120 + 1
UUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUGAUUAUGAUAGGGCCUAAAAGCGGGACGCAUCCACAAUGCACCUCCUGCAGUGCCGCUUAAGCGCUUAAAGUUGCGCAGUU
..((((((((((((((..........))))))).))))))).........(((((....((((((.((((.....))))...)))))))).)))......((((........)))).... ( -45.10)
>DroSim_CAF1 51444 120 + 1
UUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUGAUUAUGAUAGGGCCUAAAAGCGGGACGCAUCCACAAUGCACCUCCUGCAGUGCCGCUUAAGCGCUUAAAGUUGCGCAGUU
..((((((((((((((..........))))))).))))))).........(((((....((((((.((((.....))))...)))))))).)))......((((........)))).... ( -45.10)
>DroEre_CAF1 44526 120 + 1
UUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUGAUUAUGAUAGGGCCUAAAAGCGAGACGCAUCCACAAUGCACCUCCUGCAGCGCCGCUGGAGCGUUUAAGGUUUCGCAGUU
..((((((((((((((..........))))))).)))))))..................(((((((((((.....))))((((((.((......)).)))).)).....))))))).... ( -44.30)
>DroYak_CAF1 49046 120 + 1
UUUCAGGGGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUAAUUAUGAUAGGGCCUUAAAACGAGGCGCAUCUACAAUGCACCUCCUGCAGCGCUGCUAAAGCGUUUAAGGUUGCGCAGUU
....((.(((..(((.....))).(((((.((((..((((.......))))(((((.....)))))((((.....))))...)))))))))))).))...((((........)))).... ( -41.70)
>consensus
UUUCAGGUGCUUGGCAAUUUGCCUGCUGCCAGGACGCCUGAUUAUGAUAGGGCCUAAAAGCGAGACGCAUCCACAAUGCACCUCCUGCAGUGCCGCUUAAGCGCUUAAAGUUGCGCAGUU
..((((((((((((((..........))))))).))))))).........(((((...((.(((..((((.....))))..)))))..)).)))......((((........)))).... (-36.86 = -37.14 +   0.28)

alignment

secondary structure

dotplot

Window 8

Location	1,427,940 – 1,428,060
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.08
Mean single sequence MFE	-40.72
Consensus MFE	-33.34
Energy contribution	-34.06
Covariance contribution	0.72
Combinations/Pair	1.08
Mean z-score	-1.46
Structure conservation index	0.82
SVM decision value	0.23
SVM RNA-class probability	0.643092
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1427940 120 - 20766785
AACUGCGCAACUUUAAGCGCUUAAGCGGCACUGCAGGAGGUGCAUUGUGGAUGCGUCUCGCUUUUAGGCCCUGUCAUAAUCAGGCGUCCUGGCAGCAGGCAAAUUGCCAAGCACCUGAAA
..((((((........))(((.....)))...)))).((((((.(((..(((..((((.(((.((((((((((.......)))).).))))).)))))))..)))..))))))))).... ( -42.40)
>DroSec_CAF1 46394 120 - 1
AACUGCGCAACUUUAAGCGCUUAAGCGGCACUGCAGGAGGUGCAUUGUGGAUGCGUCCCGCUUUUAGGCCCUAUCAUAAUCAGGCGUCCUGGCAGCAGGCAAAUUGCCAAGCACCUGAAA
....((((........))))...((.(((.(((.(((.((((((((...)))))).))..))).)))))))).......(((((.((..((((((........)))))).)).))))).. ( -38.40)
>DroSim_CAF1 51444 120 - 1
AACUGCGCAACUUUAAGCGCUUAAGCGGCACUGCAGGAGGUGCAUUGUGGAUGCGUCCCGCUUUUAGGCCCUAUCAUAAUCAGGCGUCCUGGCAGCAGGCAAAUUGCCAAGCACCUGAAA
....((((........))))...((.(((.(((.(((.((((((((...)))))).))..))).)))))))).......(((((.((..((((((........)))))).)).))))).. ( -38.40)
>DroEre_CAF1 44526 120 - 1
AACUGCGAAACCUUAAACGCUCCAGCGGCGCUGCAGGAGGUGCAUUGUGGAUGCGUCUCGCUUUUAGGCCCUAUCAUAAUCAGGCGUCCUGGCAGCAGGCAAAUUGCCAAGCACCUGAAA
...(((............(((((((.((((((....(((..(((((...)))))..)))(((....))).............)))))))))).))).(((.....)))..)))....... ( -40.50)
>DroYak_CAF1 49046 120 - 1
AACUGCGCAACCUUAAACGCUUUAGCAGCGCUGCAGGAGGUGCAUUGUAGAUGCGCCUCGUUUUAAGGCCCUAUCAUAAUUAGGCGUCCUGGCAGCAGGCAAAUUGCCAAGCCCCUGAAA
....(((..........)))(((((..(((((((..((((((((((...))))))))))......((((((((.......)))).).))).))))).(((.....)))..))..))))). ( -43.90)
>consensus
AACUGCGCAACUUUAAGCGCUUAAGCGGCACUGCAGGAGGUGCAUUGUGGAUGCGUCUCGCUUUUAGGCCCUAUCAUAAUCAGGCGUCCUGGCAGCAGGCAAAUUGCCAAGCACCUGAAA
..((((((........))(((.....)))...)))).((((((.(((..(((..((((.(((.(((((((((.........))).).))))).)))))))..)))..))))))))).... (-33.34 = -34.06 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:55 2006