Locus 5756

Sequence ID	3L_DroMel_CAF1
Location	15,631,509 – 15,631,789
Length	280
Max. P	0.976943

overview

Window 2

Location	15,631,509 – 15,631,629
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.92
Mean single sequence MFE	-41.41
Consensus MFE	-39.58
Energy contribution	-39.83
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.97
Structure conservation index	0.96
SVM decision value	1.59
SVM RNA-class probability	0.966200
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15631509 120 - 23771897
AUUUGAAAGGAUAUGUGGCGAGGCAGCCAAAGGACAAUGCCUGGCCGCAACAUAUGCGAAAGGGAUAAUAAUUCACUGGCCGAAAGGCGAUGGGAACAAUGGUCGCAUAACUCAGGCGCG
.(((((.......((((((.(((((.((...))....))))).))))))...(((((((.((((((....)))).)).(((....)))..((....))....)))))))..))))).... ( -41.40)
>DroSec_CAF1 53758 120 - 1
AUUUGAAAGGAUAUGUGGCGAGGCAGCCAAAGGACAAUGCCUGGCCGCAACAUAUGCGAAAGGGAUAAUAAUUCACUGGCCGAAAGGCGAUGGGAACAAUGGUCGCAUAACUCAGGCGCG
.(((((.......((((((.(((((.((...))....))))).))))))...(((((((.((((((....)))).)).(((....)))..((....))....)))))))..))))).... ( -41.40)
>DroSim_CAF1 54715 120 - 1
AUUUGAAAGGAUAUGUGGCGAGGCAGCCAAAGGACAAUGCCUGGCCGCAACAUAUGCGAAAGGGAUAAUAAUUCACUGGCCGAAAGGCGAUGGGAACAAUGGUCGCAUAACUCAGGCGCG
.(((((.......((((((.(((((.((...))....))))).))))))...(((((((.((((((....)))).)).(((....)))..((....))....)))))))..))))).... ( -41.40)
>DroYak_CAF1 58392 120 - 1
AUUUGAAAGGAUUUGUGGCGAGGCAGCCGAAGGACAAUGCCGCGCCGCAACAUAUGCGAAAGGGAUAAUAACUCACUGGCCGAAAGGCGAUGGGAACAAUGGUCGCAUAACUCAGGCGCG
.(((((......((((((((.((((..(....)....)))).))))))))..(((((((............((((.(.(((....))).)))))........)))))))..))))).... ( -41.45)
>consensus
AUUUGAAAGGAUAUGUGGCGAGGCAGCCAAAGGACAAUGCCUGGCCGCAACAUAUGCGAAAGGGAUAAUAAUUCACUGGCCGAAAGGCGAUGGGAACAAUGGUCGCAUAACUCAGGCGCG
.(((((.......((((((.(((((.((...))....))))).))))))...(((((((...................(((....)))..((....))....)))))))..))))).... (-39.58 = -39.83 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	15,631,549 – 15,631,669
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.08
Mean single sequence MFE	-35.88
Consensus MFE	-33.78
Energy contribution	-34.27
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.94
SVM decision value	0.15
SVM RNA-class probability	0.607662
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15631549 120 - 23771897
GCAAAACGCCCAAUUUCCAAGGCGUGUCCGAGCAACAGACAUUUGAAAGGAUAUGUGGCGAGGCAGCCAAAGGACAAUGCCUGGCCGCAACAUAUGCGAAAGGGAUAAUAAUUCACUGGC
(((..(((((..........)))))((((...(((.......)))...)))).((((((.(((((.((...))....))))).)))))).....)))(..((((((....)))).))..) ( -36.10)
>DroSec_CAF1 53798 120 - 1
GCAAAACGCCCUAUUUCCAAGGCGUGUCCGAGCAACAGACAUUUGAAAGGAUAUGUGGCGAGGCAGCCAAAGGACAAUGCCUGGCCGCAACAUAUGCGAAAGGGAUAAUAAUUCACUGGC
(((..(((((..........)))))((((...(((.......)))...)))).((((((.(((((.((...))....))))).)))))).....)))(..((((((....)))).))..) ( -36.10)
>DroSim_CAF1 54755 120 - 1
GCAAAACGCCCAAUUUCCAAGGCGUGUCCGAGCAACAGACAUUUGAAAGGAUAUGUGGCGAGGCAGCCAAAGGACAAUGCCUGGCCGCAACAUAUGCGAAAGGGAUAAUAAUUCACUGGC
(((..(((((..........)))))((((...(((.......)))...)))).((((((.(((((.((...))....))))).)))))).....)))(..((((((....)))).))..) ( -36.10)
>DroYak_CAF1 58432 120 - 1
GCAAAACGCCCAAUUUUCAAGGCGUGUCCGAGCAACAGACAUUUGAAAGGAUUUGUGGCGAGGCAGCCGAAGGACAAUGCCGCGCCGCAACAUAUGCGAAAGGGAUAAUAACUCACUGGC
(((..(((((..........)))))((((...(((.......)))...))))((((((((.((((..(....)....)))).))))))))....)))....(((.......)))...... ( -35.20)
>consensus
GCAAAACGCCCAAUUUCCAAGGCGUGUCCGAGCAACAGACAUUUGAAAGGAUAUGUGGCGAGGCAGCCAAAGGACAAUGCCUGGCCGCAACAUAUGCGAAAGGGAUAAUAAUUCACUGGC
(((..(((((..........)))))((((...(((.......)))...)))).((((((.(((((.((...))....))))).)))))).....)))(..((((((....)))).))..) (-33.78 = -34.27 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	15,631,589 – 15,631,709
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-39.80
Consensus MFE	-37.46
Energy contribution	-37.34
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-1.54
Structure conservation index	0.94
SVM decision value	-0.05
SVM RNA-class probability	0.505753
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15631589 120 + 23771897
GCAUUGUCCUUUGGCUGCCUCGCCACAUAUCCUUUCAAAUGUCUGUUGCUCGGACACGCCUUGGAAAUUGGGCGUUUUGCAGUUAAACGUCGUUGCUGCAAAGUUUUUGGGGCGUGUUCG
(((.........(((......)))((((..........))))....))).(((((((((((..((((((.(((((((.......)))))))((....))..))))))..))))))))))) ( -39.70)
>DroSec_CAF1 53838 120 + 1
GCAUUGUCCUUUGGCUGCCUCGCCACAUAUCCUUUCAAAUGUCUGUUGCUCGGACACGCCUUGGAAAUAGGGCGUUUUGCAGUUAAACGUCGUUGCUGCAAAGUUUUUGGGGCGUGUUCG
(((.........(((......)))((((..........))))....))).(((((((((((..(((((.......((((((((...........)))))))))))))..))))))))))) ( -39.11)
>DroSim_CAF1 54795 120 + 1
GCAUUGUCCUUUGGCUGCCUCGCCACAUAUCCUUUCAAAUGUCUGUUGCUCGGACACGCCUUGGAAAUUGGGCGUUUUGCAGUUAAACGUCGUUGCUGCAAAGUUUUUGGGGCGUGUUCG
(((.........(((......)))((((..........))))....))).(((((((((((..((((((.(((((((.......)))))))((....))..))))))..))))))))))) ( -39.70)
>DroYak_CAF1 58472 120 + 1
GCAUUGUCCUUCGGCUGCCUCGCCACAAAUCCUUUCAAAUGUCUGUUGCUCGGACACGCCUUGAAAAUUGGGCGUUUUGCAGUUAAACGUCGUGGCUGCAAAGUUUUCGGGGCGUGUUCG
(((.........(((......)))...........((......)).))).((((((((((((((((((.......((((((((((.......)))))))))))))))))))))))))))) ( -40.71)
>consensus
GCAUUGUCCUUUGGCUGCCUCGCCACAUAUCCUUUCAAAUGUCUGUUGCUCGGACACGCCUUGGAAAUUGGGCGUUUUGCAGUUAAACGUCGUUGCUGCAAAGUUUUUGGGGCGUGUUCG
(((.........(((......)))((((..........))))....))).((((((((((((((((((.......((((((((...........)))))))))))))))))))))))))) (-37.46 = -37.34 +  -0.12)

alignment

secondary structure

dotplot

Window 5

Location	15,631,629 – 15,631,749
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-39.23
Consensus MFE	-36.78
Energy contribution	-36.65
Covariance contribution	-0.13
Combinations/Pair	1.05
Mean z-score	-2.82
Structure conservation index	0.94
SVM decision value	1.78
SVM RNA-class probability	0.976943
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15631629 120 + 23771897
GUCUGUUGCUCGGACACGCCUUGGAAAUUGGGCGUUUUGCAGUUAAACGUCGUUGCUGCAAAGUUUUUGGGGCGUGUUCGCCUCAUAAAUUGAUUUUUGUUUCUGUAGAAAUUUGGUUUC
(((((.....)))))((((((........)))))).(((((((...........)))))))(((((.(((((((....))))))).)))))((((...(((((....)))))..)))).. ( -37.90)
>DroSec_CAF1 53878 120 + 1
GUCUGUUGCUCGGACACGCCUUGGAAAUAGGGCGUUUUGCAGUUAAACGUCGUUGCUGCAAAGUUUUUGGGGCGUGUUCGCCUCAUAAAUUGAUUUUUGUUUCUGUAGAAAUUUGGUUUC
(((((.....)))))((((((((....)))))))).(((((((...........)))))))(((((.(((((((....))))))).)))))((((...(((((....)))))..)))).. ( -39.60)
>DroSim_CAF1 54835 120 + 1
GUCUGUUGCUCGGACACGCCUUGGAAAUUGGGCGUUUUGCAGUUAAACGUCGUUGCUGCAAAGUUUUUGGGGCGUGUUCGCCUCAUAAAUUGAUUUUUGUUUCUGUAGAAAUUUGGUUUC
(((((.....)))))((((((........)))))).(((((((...........)))))))(((((.(((((((....))))))).)))))((((...(((((....)))))..)))).. ( -37.90)
>DroYak_CAF1 58512 120 + 1
GUCUGUUGCUCGGACACGCCUUGAAAAUUGGGCGUUUUGCAGUUAAACGUCGUGGCUGCAAAGUUUUCGGGGCGUGUUCGCUUCAUAAAUUGAUUUCUGGUUCUGUAGAAAUUUGGUUUU
..........((((((((((((((((((.......((((((((((.......))))))))))))))))))))))))))))......((((..(((((((......)))))).)..)))). ( -41.51)
>consensus
GUCUGUUGCUCGGACACGCCUUGGAAAUUGGGCGUUUUGCAGUUAAACGUCGUUGCUGCAAAGUUUUUGGGGCGUGUUCGCCUCAUAAAUUGAUUUUUGUUUCUGUAGAAAUUUGGUUUC
(((((.....)))))((((((........)))))).(((((((...........)))))))(((((.(((((((....))))))).)))))((((((((......))))))))....... (-36.78 = -36.65 +  -0.13)

alignment

secondary structure

dotplot

Window 6

Location	15,631,669 – 15,631,789
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.69
Mean single sequence MFE	-17.62
Consensus MFE	-14.70
Energy contribution	-14.83
Covariance contribution	0.13
Combinations/Pair	1.11
Mean z-score	-2.31
Structure conservation index	0.83
SVM decision value	0.62
SVM RNA-class probability	0.801388
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15631669 120 - 23771897
UUCGAGGCAAAGAAAAUCUACAAAAAACCCAAAAAUAAAGGAAACCAAAUUUCUACAGAAACAAAAAUCAAUUUAUGAGGCGAACACGCCCCAAAAACUUUGCAGCAACGACGUUUAACU
...(..((((((...........................(((((.....))))).....................((.((((....)))).))....))))))..).............. ( -17.40)
>DroSec_CAF1 53918 120 - 1
UGCGAGGCAAAGAAAAUCUACAAAAAACCCAAAAAUAAAGGAAACCAAAUUUCUACAGAAACAAAAAUCAAUUUAUGAGGCGAACACGCCCCAAAAACUUUGCAGCAACGACGUUUAACU
(((...((((((...........................(((((.....))))).....................((.((((....)))).))....)))))).)))............. ( -20.00)
>DroSim_CAF1 54875 120 - 1
UGCGAAGCAAAGAAAAUCUACAAAAAACCCAAAAAUAAAAGAAACCAAAUUUCUACAGAAACAAAAAUCAAUUUAUGAGGCGAACACGCCCCAAAAACUUUGCAGCAACGACGUUUAACU
(((...((((((...........................(((((.....))))).....................((.((((....)))).))....)))))).)))............. ( -18.90)
>DroYak_CAF1 58552 119 - 1
UUCGAGGCAAAGAAAAUCUACAAA-AACCCAAAAAUAAAGAAAACCAAAUUUCUACAGAACCAGAAAUCAAUUUAUGAAGCGAACACGCCCCGAAAACUUUGCAGCCACGACGUUUAACU
.(((.(((..((.....)).....-..........(((((........((((((........))))))...........(((....)))........)))))..))).)))......... ( -14.20)
>consensus
UGCGAGGCAAAGAAAAUCUACAAAAAACCCAAAAAUAAAGGAAACCAAAUUUCUACAGAAACAAAAAUCAAUUUAUGAGGCGAACACGCCCCAAAAACUUUGCAGCAACGACGUUUAACU
...(..((((((..........................(((((......))))).....................((.((((....)))).))....))))))..).............. (-14.70 = -14.83 +   0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:59 2006