Locus 170

Sequence ID	2R_DroMel_CAF1
Location	1,428,296 – 1,428,486
Length	190
Max. P	0.994612

overview

Window 0

Location	1,428,296 – 1,428,406
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.75
Mean single sequence MFE	-36.93
Consensus MFE	-30.82
Energy contribution	-31.22
Covariance contribution	0.40
Combinations/Pair	1.19
Mean z-score	-1.43
Structure conservation index	0.83
SVM decision value	0.37
SVM RNA-class probability	0.709300
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1428296 110 + 20766785
CGCCC----------GGGACUUCACCACUCCACAAUGCGUCUACCGCGCACUUUUCCAGCGCUUUGGCUCUGGGCCGUGCUACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACAC
.((((----------((((.............(((.(((.....)))((((...(((((.((....)).)))))..)))).....)))(((......))).))))))))........... ( -36.10)
>DroSec_CAF1 46750 119 + 1
CGCCCGCUCCGCGCAGGGACUUCACCACUCCACAAUGCGUCUGCCGCGCACUUUUCCAGCGCUUUGGCUCUG-GCCAUGCUACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACAC
.((((.....(((((.(((.........)))....))))).((((((((.........))))...((...((-((((.........))))))...))))))....))))........... ( -40.00)
>DroSim_CAF1 51800 120 + 1
CGCCCGCUCCGCGCAGGGACUUCACCACUCCACAAUGCGUCUGCCGCGCAUUUUUCCAGCGCUUUGGCUCUGGGCCGUGCUACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACAC
.((((.....(((((.(((.........)))....))))).((((((((.........))))..(((((..(((........)))..))))).....))))....))))........... ( -41.10)
>DroEre_CAF1 44885 119 + 1
CGCCCGCUCCGCGCGAGGACCUCGCCACU-CACAAUGCGUCCACCGCGCACUUUUCCAGCGCUUUGGCUCUGGGCCGUGCUACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACAG
.((((.....(((((.(((((........-......).))))..)))))......((((.((....)).))))((((.((((....))))......)))).....))))........... ( -37.84)
>DroYak_CAF1 49400 120 + 1
CGCCCGCUCCGCGCGAGGACUUCACCACUCCACAAUGCGUCUACCGCGCACUUAUCCAGCGCUUUGGUUCUGGGCCCUGCUACCCUUGGCUAUCCCCGGCAUUCUGUGCUAUCCAAACAC
(((.((...)).))).(((................(((((.....))))).......(((((...(((.(((((....((((....))))....))))).)))..))))).)))...... ( -29.60)
>consensus
CGCCCGCUCCGCGCAGGGACUUCACCACUCCACAAUGCGUCUACCGCGCACUUUUCCAGCGCUUUGGCUCUGGGCCGUGCUACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACAC
.((((........(((((..................(((.....)))((((...(((((.((....)).)))))..))))...)))))(((......))).....))))........... (-30.82 = -31.22 +   0.40)

alignment

secondary structure

dotplot

Window 1

Location	1,428,326 – 1,428,446
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.67
Mean single sequence MFE	-41.38
Consensus MFE	-35.32
Energy contribution	-36.20
Covariance contribution	0.88
Combinations/Pair	1.07
Mean z-score	-2.22
Structure conservation index	0.85
SVM decision value	2.49
SVM RNA-class probability	0.994612
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1428326 120 + 20766785
CUACCGCGCACUUUUCCAGCGCUUUGGCUCUGGGCCGUGCUACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACACCCAGUCACAGCCGGCACUGGUCACCUAUGUGACGACCUCG
....(((((((...(((((.((....)).)))))..))))......((((((...(((((...(((((...........))))).....)))))...)))))).....)))......... ( -41.30)
>DroSec_CAF1 46790 119 + 1
CUGCCGCGCACUUUUCCAGCGCUUUGGCUCUG-GCCAUGCUACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACACCCAGCCACAGCCGGCACUGGUCACCUAUGUGACCACCUCG
.((((((((.........))))...((((.((-((((.........)))))).....(((....((((...........)))))))..)))))))).(((((((....)))))))..... ( -44.30)
>DroSim_CAF1 51840 120 + 1
CUGCCGCGCAUUUUUCCAGCGCUUUGGCUCUGGGCCGUGCUACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACACCCAGCCACAGCCGGCACUGGUCACCUAUGUGACCACCUCG
.((((((((.........))))...((((.(((((((.((((....))))......))))...(((((...........)))))))).)))))))).(((((((....)))))))..... ( -45.80)
>DroEre_CAF1 44924 120 + 1
CCACCGCGCACUUUUCCAGCGCUUUGGCUCUGGGCCGUGCUACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACAGCCAGGCACCGCCGGCGCUGGUCACCUAUAUGACCACCUCG
.....((((.......(((.((....)).)))(((.(((((.......(((......)))......((((........)))).))))).))).))))((((((......))))))..... ( -43.50)
>DroYak_CAF1 49440 120 + 1
CUACCGCGCACUUAUCCAGCGCUUUGGUUCUGGGCCCUGCUACCCUUGGCUAUCCCCGGCAUUCUGUGCUAUCCAAACACCCAGCCACAGCCGGCACUGGUCAGCUAUGUGACCACCUCG
.....((((.........))))(((((....(((....((((....))))....)))(((((...)))))..)))))......(((......)))..((((((......))))))..... ( -32.00)
>consensus
CUACCGCGCACUUUUCCAGCGCUUUGGCUCUGGGCCGUGCUACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACACCCAGCCACAGCCGGCACUGGUCACCUAUGUGACCACCUCG
.....((((.........))))..(((((..(((........)))..)))))...(((((...(((((...........))))).....)))))...(((((((....)))))))..... (-35.32 = -36.20 +   0.88)

alignment

secondary structure

dotplot

Window 2

Location	1,428,326 – 1,428,446
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.67
Mean single sequence MFE	-51.40
Consensus MFE	-43.10
Energy contribution	-43.62
Covariance contribution	0.52
Combinations/Pair	1.12
Mean z-score	-2.15
Structure conservation index	0.84
SVM decision value	2.09
SVM RNA-class probability	0.987632
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1428326 120 - 20766785
CGAGGUCGUCACAUAGGUGACCAGUGCCGGCUGUGACUGGGUGUUUGGAUAGCCCAGAAUGCCGGGGGUGGCCAAGGGUAGCACGGCCCAGAGCCAAAGCGCUGGAAAAGUGCGCGGUAG
...((((..(.....)..))))..((((((((.((.((((((.........))))))...((((...((.(((...))).)).)))).)).))))...(((((.....)))))..)))). ( -49.60)
>DroSec_CAF1 46790 119 - 1
CGAGGUGGUCACAUAGGUGACCAGUGCCGGCUGUGGCUGGGUGUUUGGAUAGCCCAGAAUGCCGGGGGUGGCCAAGGGUAGCAUGGC-CAGAGCCAAAGCGCUGGAAAAGUGCGCGGCAG
.....(((((((....))))))).((((((((.(((((..((.(((((...((((.(.....)..))))..)))))....))..)))-)).))))...(((((.....)))))..)))). ( -54.80)
>DroSim_CAF1 51840 120 - 1
CGAGGUGGUCACAUAGGUGACCAGUGCCGGCUGUGGCUGGGUGUUUGGAUAGCCCAGAAUGCCGGGGGUGGCCAAGGGUAGCACGGCCCAGAGCCAAAGCGCUGGAAAAAUGCGCGGCAG
.....(((((((....))))))).((((((((.(((((((((.........))))))...((((...((.(((...))).)).))))))).))))...((((.........)))))))). ( -56.00)
>DroEre_CAF1 44924 120 - 1
CGAGGUGGUCAUAUAGGUGACCAGCGCCGGCGGUGCCUGGCUGUUUGGAUAGCCCAGAAUGCCGGGGGUGGCCAAGGGUAGCACGGCCCAGAGCCAAAGCGCUGGAAAAGUGCGCGGUGG
...(.(((((((....))))))).)((((((.((.((((((..(((((.....)))))..)))))).)).))).......((((...((((.((....)).))))....))))..))).. ( -53.80)
>DroYak_CAF1 49440 120 - 1
CGAGGUGGUCACAUAGCUGACCAGUGCCGGCUGUGGCUGGGUGUUUGGAUAGCACAGAAUGCCGGGGAUAGCCAAGGGUAGCAGGGCCCAGAACCAAAGCGCUGGAUAAGUGCGCGGUAG
...((((((((......)))))...)))((((((..((((...((((.......))))...))))..))))))..((((......))))...(((...(((((.....)))))..))).. ( -42.80)
>consensus
CGAGGUGGUCACAUAGGUGACCAGUGCCGGCUGUGGCUGGGUGUUUGGAUAGCCCAGAAUGCCGGGGGUGGCCAAGGGUAGCACGGCCCAGAGCCAAAGCGCUGGAAAAGUGCGCGGUAG
...(((((((((....))))))..(.(((((.....((((((.........))))))...))))).)...)))..((((......))))...(((...(((((.....)))))..))).. (-43.10 = -43.62 +   0.52)

alignment

secondary structure

dotplot

Window 3

Location	1,428,366 – 1,428,486
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.58
Mean single sequence MFE	-39.24
Consensus MFE	-32.02
Energy contribution	-32.70
Covariance contribution	0.68
Combinations/Pair	1.07
Mean z-score	-2.00
Structure conservation index	0.82
SVM decision value	1.47
SVM RNA-class probability	0.956873
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1428366 120 + 20766785
UACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACACCCAGUCACAGCCGGCACUGGUCACCUAUGUGACGACCUCGUCGUCGUCCAGUCAGCGGGGCCACUCCGCCAGUCCGCACC
......((((((...(((((...(((((...........))))).....)))))...))))))....((.((((((......))))))))....(((((((......)))...))))... ( -43.40)
>DroSec_CAF1 46829 120 + 1
UACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACACCCAGCCACAGCCGGCACUGGUCACCUAUGUGACCACCUCGUCGUCGUCCAGUCAGCGGAGCCACUCCGCCAGUCCGCACA
.......(((.....(((((...(((((...........))))).....)))))...(((((((....)))))))....)))((((..(.....((((((...))))))..)..)).)). ( -37.30)
>DroSim_CAF1 51880 120 + 1
UACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACACCCAGCCACAGCCGGCACUGGUCACCUAUGUGACCACCUCGUCGUCGUCCAGCCAGCGGAGCCACUCCGCCAGUCCGCACC
......((((.....(((((...(((((...........))))).....)))))...(((((((....)))))))...............))))((((((...))))))........... ( -39.30)
>DroEre_CAF1 44964 120 + 1
UACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACAGCCAGGCACCGCCGGCGCUGGUCACCUAUAUGACCACCUCGUCGACGUCCAGUCAGCGGAGCCACUCCGCCAGUCCGCACC
.....(((((.......(((....(((.....)))....))).(((.((((.((((.((((((......))))))...))))(((.....))).)))).))).....)))))........ ( -41.50)
>DroYak_CAF1 49480 120 + 1
UACCCUUGGCUAUCCCCGGCAUUCUGUGCUAUCCAAACACCCAGCCACAGCCGGCACUGGUCAGCUAUGUGACCACCUCGACGAAGUCAAGUCAGCGGAGCCACUCCGCCAGUUCAAUCC
....(((((((.((.(((((....((((((............)).)))))))))...((((((......)))))).......)))))))))...((((((...))))))........... ( -34.70)
>consensus
UACCCUUGGCCACCCCCGGCAUUCUGGGCUAUCCAAACACCCAGCCACAGCCGGCACUGGUCACCUAUGUGACCACCUCGUCGUCGUCCAGUCAGCGGAGCCACUCCGCCAGUCCGCACC
......((((.....(((((...(((((...........))))).....)))))...(((((((....)))))))...............))))((((((...))))))........... (-32.02 = -32.70 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:00 2006