Locus 5895

Sequence ID	3L_DroMel_CAF1
Location	15,841,866 – 15,842,016
Length	150
Max. P	0.769699

overview

Window 4

Location	15,841,866 – 15,841,956
Length	90
Sequences	4
Columns	96
Reading direction	reverse
Mean pairwise identity	92.11
Mean single sequence MFE	-22.81
Consensus MFE	-17.57
Energy contribution	-18.07
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.94
Structure conservation index	0.77
SVM decision value	0.32
SVM RNA-class probability	0.686282
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15841866 90 - 23771897
CAACACGCGUGACCAGCAGCAUAAGCCCACCCAACUUCCAUU----UUGCA-ACUGCCACGCCCACAUCCCAUUGGGG-CCGUCAGCCCACCGUGA
...((((((((..(((..(((.....................----.))).-.))).))))).............(((-(.....))))...))). ( -21.75)
>DroSec_CAF1 48949 92 - 1
CAACACGCGUGACCAGCAGCAUAAGCCCACCCAACUUCCAUU----UUGCAAACUGCCACGCCCACAUCCCAGUGGCCCCCAUCAGCCCACCGUGA
...((((.(((....((.(((.....................----.))).....(((((............)))))........)).))))))). ( -17.95)
>DroEre_CAF1 48109 94 - 1
CAACACGCGUGACCAGCAGCAUAAGCCCACCCAGCUUCCACUUCCAUUGCA-GCUGCCACGCCCACAUCCCAGUGGGG-CCUUCAGCCCACCGUGA
...((((((((..((((.(((.((((.......))))..........))).-)))).))))).(((......)))(((-(.....))))...))). ( -28.20)
>DroYak_CAF1 90375 90 - 1
CAACACGCGUGACCAGCAGCAUAAGCCCACCCAACUUUCAUU----UUGCA-ACUGCCACGCCCACAUCCCAGUGGGG-CCUUCAGCCCACCGUGA
...((((((((..(((..(((.....................----.))).-.))).))))).(((......)))(((-(.....))))...))). ( -23.35)
>consensus
CAACACGCGUGACCAGCAGCAUAAGCCCACCCAACUUCCAUU____UUGCA_ACUGCCACGCCCACAUCCCAGUGGGG_CCUUCAGCCCACCGUGA
...((((((((..(((..(((..........................)))...))).)))))..........(((((.........))))).))). (-17.57 = -18.07 +   0.50)

alignment

secondary structure

dotplot

Window 5

Location	15,841,891 – 15,841,993
Length	102
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	95.22
Mean single sequence MFE	-37.42
Consensus MFE	-37.39
Energy contribution	-37.33
Covariance contribution	-0.06
Combinations/Pair	1.07
Mean z-score	-1.48
Structure conservation index	1.00
SVM decision value	0.42
SVM RNA-class probability	0.728591
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15841891 102 + 23771897
GGAUGUGGGCGUGGCAGU-UGCAA----AAUGGAAGUUGGGUGGGCUUAUGCUGCUGGUCACGCGUGUUGGCCGCGUGUGUCCUGCGCUGAUUUCGCCAUAAUAAAU
...(((((.(((.((...-.))..----.)))(((((..(...(((....)))((.((.((((((((.....)))))))).)).)).)..))))).)))))...... ( -36.50)
>DroSec_CAF1 48975 103 + 1
GGAUGUGGGCGUGGCAGUUUGCAA----AAUGGAAGUUGGGUGGGCUUAUGCUGCUGGUCACGCGUGUUGGCCGCGUGUGUCCUGCGCUGAUUUCGCCAUAAUAAAU
((.((..(((......)))..)).----....(((((..(...(((....)))((.((.((((((((.....)))))))).)).)).)..))))).))......... ( -36.60)
>DroEre_CAF1 48134 106 + 1
GGAUGUGGGCGUGGCAGC-UGCAAUGGAAGUGGAAGCUGGGUGGGCUUAUGCUGCUGGUCACGCGUGUUGGCCGCGUGUGUCCUGCGCUGAUUUCGCCAUAAUAAAU
((..((.(((((((((((-.((......(((....)))......))....))))))((.((((((((.....)))))))).)).))))).))....))......... ( -39.80)
>DroYak_CAF1 90400 102 + 1
GGAUGUGGGCGUGGCAGU-UGCAA----AAUGAAAGUUGGGUGGGCUUAUGCUGCUGGUCACGCGUGUUGGUCGCGUGUGUCCUGCGCUGAUUUCGCCAUAAUAAAU
((..((.(((((((((((-.((..----(((....)))......))....))))))((.((((((((.....)))))))).)).))))).))....))......... ( -36.80)
>consensus
GGAUGUGGGCGUGGCAGU_UGCAA____AAUGGAAGUUGGGUGGGCUUAUGCUGCUGGUCACGCGUGUUGGCCGCGUGUGUCCUGCGCUGAUUUCGCCAUAAUAAAU
((..((.(((((((((((..((......(((....)))......))....))))))((.((((((((.....)))))))).)).))))).))....))......... (-37.39 = -37.33 +  -0.06)

alignment

secondary structure

dotplot

Window 6

Location	15,841,891 – 15,841,993
Length	102
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	95.22
Mean single sequence MFE	-24.47
Consensus MFE	-22.77
Energy contribution	-22.77
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.93
SVM decision value	0.53
SVM RNA-class probability	0.769699
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15841891 102 - 23771897
AUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGGCCAACACGCGUGACCAGCAGCAUAAGCCCACCCAACUUCCAUU----UUGCA-ACUGCCACGCCCACAUCC
.........((((....(((.((((((..((((((.......)))))).......((....))..............))----)))).-.)))...))))....... ( -23.60)
>DroSec_CAF1 48975 103 - 1
AUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGGCCAACACGCGUGACCAGCAGCAUAAGCCCACCCAACUUCCAUU----UUGCAAACUGCCACGCCCACAUCC
.........((((....(((.((((((..((((((.......)))))).......((....))..............))----))))...)))...))))....... ( -23.20)
>DroEre_CAF1 48134 106 - 1
AUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGGCCAACACGCGUGACCAGCAGCAUAAGCCCACCCAGCUUCCACUUCCAUUGCA-GCUGCCACGCCCACAUCC
.........((((....((((((((((..((((((.......))))))...........((((.......)))).....)))..))).-))))...))))....... ( -28.80)
>DroYak_CAF1 90400 102 - 1
AUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGACCAACACGCGUGACCAGCAGCAUAAGCCCACCCAACUUUCAUU----UUGCA-ACUGCCACGCCCACAUCC
.........((((....(((.((((((..((((((.......)))))).......((....))..............))----)))).-.)))...))))....... ( -22.30)
>consensus
AUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGGCCAACACGCGUGACCAGCAGCAUAAGCCCACCCAACUUCCAUU____UUGCA_ACUGCCACGCCCACAUCC
.........((((......((((.((...((((((.......)))))).)).)).))............................((.....))..))))....... (-22.77 = -22.77 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	15,841,926 – 15,842,016
Length	90
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	94.49
Mean single sequence MFE	-21.02
Consensus MFE	-18.47
Energy contribution	-18.47
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.27
Structure conservation index	0.88
SVM decision value	0.31
SVM RNA-class probability	0.681154
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15841926 90 - 23771897
AGAGAAAUGUCCAAAAAAUGUCAAUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGGC-----------CAACACGCGUGACCAGCAGCAUAAGCCCAC
.......(((((...((((....))))......(((.......))).)))))((((((..-----------.....)))))).......((....)).... ( -20.60)
>DroSec_CAF1 49011 90 - 1
AGAGAAAUGUCCAAAAAAUGUCAAUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGGC-----------CAACACGCGUGACCAGCAGCAUAAGCCCAC
.......(((((...((((....))))......(((.......))).)))))((((((..-----------.....)))))).......((....)).... ( -20.60)
>DroSim_CAF1 50202 101 - 1
AGAGAAAUGUCCAAAAAAUGUCAAUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGGCCAACACGCGGCCAACACGCGUGACCAGCAGCAUAAGCCCAC
.......(((((...((((....))))......(((.......))).)))))...((.((...((((((.......))))))....)).)).......... ( -24.40)
>DroEre_CAF1 48173 90 - 1
AGAGAAACGUCCAAAAAAUGUCAAUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGGC-----------CAACACGCGUGACCAGCAGCAUAAGCCCAC
........((((...((((....))))......(((.......))).)))).((((((..-----------.....)))))).......((....)).... ( -20.20)
>DroYak_CAF1 90435 90 - 1
AGAGAAAUGUCCAAAAAAUGUCAAUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGAC-----------CAACACGCGUGACCAGCAGCAUAAGCCCAC
.......(((((...((((....))))......(((.......))).)))))((((((..-----------.....)))))).......((....)).... ( -19.30)
>consensus
AGAGAAAUGUCCAAAAAAUGUCAAUUUAUUAUGGCGAAAUCAGCGCAGGACACACGCGGC___________CAACACGCGUGACCAGCAGCAUAAGCCCAC
........((((...((((....))))......(((.......))).)))).((((((..................)))))).......((....)).... (-18.47 = -18.47 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:11 2006