Locus 1794

Sequence ID	3L_DroMel_CAF1
Location	5,072,547 – 5,072,900
Length	353
Max. P	0.766405

overview

Window 3

Location	5,072,547 – 5,072,667
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.72
Mean single sequence MFE	-21.36
Consensus MFE	-16.26
Energy contribution	-16.62
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-1.86
Structure conservation index	0.76
SVM decision value	0.23
SVM RNA-class probability	0.644689
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5072547 120 + 23771897
AAAACAAAACAAAGCUAAGCGAAGAAUGGAAAAAACAAUCUUUUCAUAAAAUCACGCAAACGCGGCGCUGAAUAAGCUGGCAAACCUAAACAACAAUGCAAUUUUUACUGUUUGUCGCCU
............((((.((((....(((((((........))))))).......(((....))).)))).....))))(((((((.((((.............))))..))))))).... ( -20.42)
>DroSec_CAF1 279053 120 + 1
AAAACAAAACAAAGCGAAGCGAAGAAUGGAAAAAACAAUCUUUUCAUAAAAUCACGCAAACGCGGCGCUGAAUAAGCUGGCAAACCUAAACAACAAUGCAAUUUUUACUGUUUGUCGCCU
.............(((..(((..(((((((((........)))))))....)).)))...)))((((((.....))).(((((((.((((.............))))..)))))))))). ( -23.12)
>DroSim_CAF1 300342 120 + 1
AAAACAAAACAAAGCGAAGCGAAGAAUGGAAAAAACAAUCUUUUCAUAAAAUCACGCAAACGCGGCGCUGAAUAAGCUGGCAAACCUAAACAACAAUGCAAUUUUUACUGUUUGUCGCCU
.............(((..(((..(((((((((........)))))))....)).)))...)))((((((.....))).(((((((.((((.............))))..)))))))))). ( -23.12)
>DroEre_CAF1 285977 115 + 1
AUAACAAAACAAAGCG-----CAGAAUAGAAAAAACAAUCUUUUCAUAAAAUCACGCAAACGCGGCGCUGAAUAAGCUGGCAAACCUAAACAACAAUGCAAUUUUUACUGUUUGUCGCCU
............((((-----(.(((.(((........))).))).........(((....))))))))......((.(((((((.((((.............))))..))))))))).. ( -21.92)
>DroYak_CAF1 289960 110 + 1
AAAGCAAAACAAAGCG----------UAGAAACAACAAUCUUUUCAUAAAAUCACGCAAACGCGGCGCUGAAUAAGCUGGCAAACCUAAACAACAAUGCAAUUUUUACUGUUUGUCGCCU
..(((.......((((----------(.((((.........)))).........(((....))))))))......)))(((((((.((((.............))))..))))))).... ( -18.24)
>consensus
AAAACAAAACAAAGCGAAGCGAAGAAUGGAAAAAACAAUCUUUUCAUAAAAUCACGCAAACGCGGCGCUGAAUAAGCUGGCAAACCUAAACAACAAUGCAAUUUUUACUGUUUGUCGCCU
.......................(((.(((........))).)))..........((....))((((((.....))).(((((((.((((.............))))..)))))))))). (-16.26 = -16.62 +   0.36)

alignment

secondary structure

dotplot

Window 4

Location	5,072,587 – 5,072,701
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.73
Mean single sequence MFE	-31.48
Consensus MFE	-27.72
Energy contribution	-28.00
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-1.20
Structure conservation index	0.88
SVM decision value	0.09
SVM RNA-class probability	0.579750
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5072587 114 - 23771897
CAAAAGAGAGGGGGCGAAGUGUG--UGUG----UGUGAGUAGGCGACAAACAGUAAAAAUUGCAUUGUUGUUUAGGUUUGCCAGCUUAUUCAGCGCCGCGUUUGCGUGAUUUUAUGAAAA
.....((((..(.(((((.((((--.(((----(.((((((((((((((.((((....))))..))))).....((....)).)))))))))))))))))))))).)..))))....... ( -32.50)
>DroSec_CAF1 279093 116 - 1
CGAAAGAGAGGGGGCGAAGUGUGCGUGUG----UGUGAGUAGGCGACAAACAGUAAAAAUUGCAUUGUUGUUUAGGUUUGCCAGCUUAUUCAGCGCCGCGUUUGCGUGAUUUUAUGAAAA
.....((((..(.((((((((.((((.((----.(((((((((((((((.((((....))))..))))))))).((....)).)))))).))))))))).))))).)..))))....... ( -32.60)
>DroSim_CAF1 300382 116 - 1
CGAAAGAGAGGGGGCGAAGUGUGCGUGUG----UGUGAGUAGGCGACAAACAGUAAAAAUUGCAUUGUUGUUUAGGUUUGCCAGCUUAUUCAGCGCCGCGUUUGCGUGAUUUUAUGAAAA
.....((((..(.((((((((.((((.((----.(((((((((((((((.((((....))))..))))))))).((....)).)))))).))))))))).))))).)..))))....... ( -32.60)
>DroEre_CAF1 286012 112 - 1
CGAAAGAGAGGGGGCGAAGUGUGUGUG--------UGAGUAGGCGACAAACAGUAAAAAUUGCAUUGUUGUUUAGGUUUGCCAGCUUAUUCAGCGCCGCGUUUGCGUGAUUUUAUGAAAA
.....((((..(.((((((((.((((.--------((((((((((((((.((((....))))..))))).....((....)).)))))))))))))))).))))).)..))))....... ( -31.80)
>DroYak_CAF1 289990 120 - 1
GAAAAGAGAGGGGGCGGAGUGUGUGUGUGUGCGUGUGUGUAGGCGACAAACAGUAAAAAUUGCAUUGUUGUUUAGGUUUGCCAGCUUAUUCAGCGCCGCGUUUGCGUGAUUUUAUGAAAA
.....((((..(.(((((.((((.((((.((.(((.((.((((((((((.((((....))))..))))))))))((....)).)).))).))))))))))))))).)..))))....... ( -27.90)
>consensus
CGAAAGAGAGGGGGCGAAGUGUGCGUGUG____UGUGAGUAGGCGACAAACAGUAAAAAUUGCAUUGUUGUUUAGGUUUGCCAGCUUAUUCAGCGCCGCGUUUGCGUGAUUUUAUGAAAA
.....((((..(.((((((((.((((.........((((((((((((((.((((....))))..))))).....((....)).)))))))))))))))).))))).)..))))....... (-27.72 = -28.00 +   0.28)

alignment

secondary structure

dotplot

Window 5

Location	5,072,701 – 5,072,820
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.71
Mean single sequence MFE	-27.32
Consensus MFE	-19.76
Energy contribution	-20.16
Covariance contribution	0.40
Combinations/Pair	1.09
Mean z-score	-2.11
Structure conservation index	0.72
SVM decision value	0.24
SVM RNA-class probability	0.649314
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5072701 119 + 23771897
CUAGCAAUCAGCCCGUCUCUUUCGCACCCACCU-ACUACCAUCUCACUCACUCCAACGUGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAU
..........(((((.(((((((((........-............(((((......))))).....(((((......))))))).)).))))))))..))................... ( -25.00)
>DroSec_CAF1 279209 119 + 1
CUCGCAAUCAGCCCGUCUCUUUCGCACCCGCCU-ACUGCCAUCCCACUCACUCCAACGUGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAU
..........(((((.(((((..((....))..-.(((((......(((((......)))))......((((......)))))))))..))))))))..))................... ( -31.80)
>DroSim_CAF1 300498 119 + 1
CUUGCAAUCAGCCUGUCUCUUUCGCACCCACCU-ACCGCCAUCUCACUCACUCCAAUGUGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAU
.((((.....((...........))........-...(((......(((((......)))))((.((((..((((.......))))..)))).))))).))))................. ( -27.90)
>DroEre_CAF1 286124 119 + 1
CUCGCAAUCAGCCCAUCUCUGUCACACCCACGC-ACAGCCCUCUCACUCACUCCAACGCGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCGAAACAUUUAAAUCAAAAU
.((((.....(((...(((((((........((-(.((.((((.(............).))))..))))).((((.......))))))).)))).))).))))................. ( -24.80)
>DroYak_CAF1 290110 120 + 1
CACGCAAUGAGGCCGUCUCUUUCACACCCAUCCAACAGCUAUCUCACACACUCCAACGUGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAU
.......((..((((.(((((((...................(((((..........)))))((....((((......)))).)).)).)))))))))..)).................. ( -27.10)
>consensus
CUCGCAAUCAGCCCGUCUCUUUCGCACCCACCU_ACAGCCAUCUCACUCACUCCAACGUGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAU
...((.........((.......))............(((......(((((......)))))((.((((..((((.......))))..)))).))))).))................... (-19.76 = -20.16 +   0.40)

alignment

secondary structure

dotplot

Window 6

Location	5,072,740 – 5,072,860
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-30.30
Consensus MFE	-28.54
Energy contribution	-28.74
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.26
Structure conservation index	0.94
SVM decision value	0.29
SVM RNA-class probability	0.672291
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5072740 120 + 23771897
AUCUCACUCACUCCAACGUGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGU
......(((((......)))))(.(((((((((.....(((((((........((....))....(((((......))))).....)))))))((((.....))))))))))))).)... ( -30.00)
>DroSec_CAF1 279248 120 + 1
AUCCCACUCACUCCAACGUGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGU
......(((((......)))))(.(((((((((.....(((((((........((....))....(((((......))))).....)))))))((((.....))))))))))))).)... ( -30.00)
>DroSim_CAF1 300537 120 + 1
AUCUCACUCACUCCAAUGUGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGU
......(((((......)))))(.(((((((((.....(((((((........((....))....(((((......))))).....)))))))((((.....))))))))))))).)... ( -30.60)
>DroEre_CAF1 286163 120 + 1
CUCUCACUCACUCCAACGCGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCGAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGU
(((.((...((((..((.((((((.((((..((((.......))))..)))).)).(((((....(((((......))))).....)))))...)))).)).))))..)).)))...... ( -31.10)
>DroYak_CAF1 290150 120 + 1
AUCUCACACACUCCAACGUGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGU
........(((......)))(((.(((((((((.....(((((((........((....))....(((((......))))).....)))))))((((.....)))))))))))))))).. ( -29.80)
>consensus
AUCUCACUCACUCCAACGUGAGGCACUUGCAUGUCACAAUGCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGU
........(((......)))(((.(((((((((.....(((((((........((....))....(((((......))))).....)))))))((((.....)))))))))))))))).. (-28.54 = -28.74 +   0.20)

alignment

secondary structure

dotplot

Window 7

Location	5,072,780 – 5,072,900
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.83
Mean single sequence MFE	-26.50
Consensus MFE	-24.04
Energy contribution	-24.12
Covariance contribution	0.08
Combinations/Pair	1.04
Mean z-score	-1.25
Structure conservation index	0.91
SVM decision value	0.52
SVM RNA-class probability	0.766405
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5072780 120 + 23771897
GCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGUGAAGGAAAAGCGGGUGGAAAACCAGAGGGGCCGUGGGAGA
(((((...((((....(((((....(((((......))))).....)))))...))))..........(((...((((....))))...)))(((.....)))......)))))...... ( -30.90)
>DroSec_CAF1 279288 120 + 1
GCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGUGAAGGAAAAGCGGGUGGAAAACCAGAGGGGGCGAGGGAGA
(((((........((....))....(((((......))))).....)))))...((((..........(((...((((....))))...)))(((.....)))........))))..... ( -25.20)
>DroSim_CAF1 300577 120 + 1
GCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGUGAAGGAAAAGCGGGUGGAAAACCAGAGGGGGCGAGGGAAA
(((((........((....))....(((((......))))).....)))))...((((..........(((...((((....))))...)))(((.....)))........))))..... ( -25.20)
>DroEre_CAF1 286203 120 + 1
GCGGCAGACAAGAGCGGCAGCGAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGUGAAGGAAAAGCGGGCGGAAAACCGGAGAGGGGGGGGAUAA
.(.((...((((....(((((....(((((......))))).....)))))...))))..........(((...((((....))))...))).)).)....((.....)).......... ( -25.40)
>DroYak_CAF1 290190 114 + 1
GCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGUGAAGGAAAAGCGGGUGGAAAGCCAGAGGGGUGGA------
..(((...((((....(((((....(((((......))))).....)))))...)))).......((((.((..((((....))))....)).))))...)))...........------ ( -25.80)
>consensus
GCGGCAGACAAGAGCGGCAGCAAAACAUUUAAAUCAAAAUGAUAAAGUUGCAUACUUGAGUAGAGUUAUGCGAGUCCUGUGAAGGAAAAGCGGGUGGAAAACCAGAGGGGGCGAGGGAAA
((.((........)).)).((....(((((......)))))......((((((((((.....))).))))))).((((....))))...)).(((.....)))................. (-24.04 = -24.12 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:42 2006