Locus 652

Sequence ID	2L_DroMel_CAF1
Location	1,952,172 – 1,952,489
Length	317
Max. P	0.906725

overview

Window 7

Location	1,952,172 – 1,952,289
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.22
Mean single sequence MFE	-55.95
Consensus MFE	-40.10
Energy contribution	-42.35
Covariance contribution	2.25
Combinations/Pair	1.14
Mean z-score	-2.33
Structure conservation index	0.72
SVM decision value	1.05
SVM RNA-class probability	0.906725
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1952172 117 - 22407834
CUUCACCGCAUCCCUGAAUGCCAGCUUGCAUCACUCGCAGUCGCUGAGAAGAAAUCUGGGUCAUCCACUGGCCGCGGCAGCUGCCGUGGCGGCAGUGGCCCAAUCCCAGGCGG---UGCC
...((((((............((((((((.......))))..)))).........(((((....((((((((((((((....))))))))..))))))......)))))))))---)).. ( -52.70)
>DroEre_CAF1 3821 117 - 1
CUUCACCGCCUCCCUGAACGCCAGCUUGCAUCACUCGCAGUCGCUGAGAAGGAAUCUGGGCCAUCCUCUGGCCGCGGCAGCUGCGGUGGCGGCGGCGGCCCAGUCCCAGGCGG---UGCC
...((((((((..(((..((((.(((.((..(((.((((((.(((((((.....))).(((((.....))))).)))).))))))))))))))))))...)))....))))))---)).. ( -57.10)
>DroYak_CAF1 1393 117 - 1
CUUCACCGCCUCCCUGAACGCCAGCCUGCAUCACUCGCAGUCGCUGCGAAGGAAUCUGGGUCAUCCGCUGGCCGCGGCUGCUGCCGUGGCGGCGGCUGCCCAAUCCCAGGCGG---UGCC
...((((((((.(((...(((.(((((((.......))))..)))))).)))....((((.((.((((((.(((((((....))))))))))))).)))))).....))))))---)).. ( -63.70)
>DroAna_CAF1 24008 120 - 1
CUUCACCGCCUCGCUGAACGCCAGUCUCCACCACUCGCAGUCGCUGCGCCGCAAUCUGGGCCAUCCUUUGGCUGCAGCAGCCGCCGCAGCGGCCGUGGCACAGUCCCAGGCGGUAGUGCC
....(((((((.((((...((((((.......))).((.((((((((((.((...((((((((.....))))).)))..)).).))))))))).))))).))))...)))))))...... ( -50.30)
>consensus
CUUCACCGCCUCCCUGAACGCCAGCCUGCAUCACUCGCAGUCGCUGAGAAGGAAUCUGGGCCAUCCUCUGGCCGCGGCAGCUGCCGUGGCGGCGGCGGCCCAAUCCCAGGCGG___UGCC
.....((((((..........((((((((.......))))..))))....((...((((((((((...(.((((((((....)))))))).).))))))))))..))))))))....... (-40.10 = -42.35 +   2.25)

alignment

secondary structure

dotplot

Window 8

Location	1,952,249 – 1,952,369
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	87.92
Mean single sequence MFE	-55.80
Consensus MFE	-45.59
Energy contribution	-47.40
Covariance contribution	1.81
Combinations/Pair	1.15
Mean z-score	-1.47
Structure conservation index	0.82
SVM decision value	0.13
SVM RNA-class probability	0.599297
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1952249 120 + 22407834
CUGCGAGUGAUGCAAGCUGGCAUUCAGGGAUGCGGUGAAGCUGCUCAGGUGGGCGGCGCUGGCCAGCGAUUGCUGUUGGGCGGUAAGGGCUGCAUAUUGGGCGGCAGCAGCGGCGCACAU
......(((.(((..(((((((((....)))))......(((((((((....(((((((((.((((((.....)))))).))))....)))))...)))))))))..)))).)))))).. ( -54.60)
>DroEre_CAF1 3898 120 + 1
CUGCGAGUGAUGCAAGCUGGCGUUCAGGGAGGCGGUGAAGCUGCUCAGGUGGGCGGCGCUGGCCAGCGAUUGCUGUUGGGCGGUCAGGGCCGCAUACUGGGCGGCAGCGGCGGCGCACAU
......(((.(((..((((.(((((((....(((((...(((((((....)))))))((((.((((((.....)))))).))))....)))))...))))))).))))....)))))).. ( -61.60)
>DroYak_CAF1 1470 120 + 1
CUGCGAGUGAUGCAGGCUGGCGUUCAGGGAGGCGGUGAAGCUGCUCAGGUGGGCGGCGCUGGCCAGCGAUUGCUGUUGGGCGGUCAGGGCCGCGUAUUGGGCGGCGGCGGCGGCGCACAU
.((((.....(((..((((.(((((((..(.(((((...(((((((....)))))))((((.((((((.....)))))).))))....))))).).))))))).)))).))).))))... ( -59.60)
>DroAna_CAF1 24088 111 + 1
CUGCGAGUGGUGGAGACUGGCGUUCAGCGAGGCGGUGAAGCUGCUCAGGUGGG---------UCAGCGACUGCUGCUGGGCAGUCAGGGCGGCGUACUGGGCGGCGGCGGCGGCACACAU
......(((((.(...((((((((((((..((((((...(((((((....)))---------.)))).))))))))))))).)))))(.((.(((.....))).)).)..).)).))).. ( -47.40)
>consensus
CUGCGAGUGAUGCAAGCUGGCGUUCAGGGAGGCGGUGAAGCUGCUCAGGUGGGCGGCGCUGGCCAGCGAUUGCUGUUGGGCGGUCAGGGCCGCAUACUGGGCGGCAGCGGCGGCGCACAU
......(((.(((..((((.(((((((..(.(((((...(((((((....)))))))((((.((((((.....)))))).))))....))))).).))))))).)))).))).))).... (-45.59 = -47.40 +   1.81)

alignment

secondary structure

dotplot

Window 9

Location	1,952,369 – 1,952,489
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.33
Mean single sequence MFE	-51.55
Consensus MFE	-43.20
Energy contribution	-43.32
Covariance contribution	0.12
Combinations/Pair	1.18
Mean z-score	-1.54
Structure conservation index	0.84
SVM decision value	0.24
SVM RNA-class probability	0.649746
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1952369 120 + 22407834
CAGCUGAUUGGGUGCAUAGUACAGCAGGGGAUACUGCGAGAGCAGCUCCUGGUGGCGGGAGCUCACAAACUGCUGCACAGCAGCGGUGCUCGGCGGCGAGGCCACCGAUGAAGUGGCGCC
..((((.....(((((((((....((((((...((((....))))))))))(((((....)).)))..)))).)))))..))))(((((((((.(((...))).)))).......))))) ( -54.51)
>DroEre_CAF1 4018 120 + 1
CAGCUGAUUGGGUGCAUAGUAGAGCAGGGGAUACUGCGAGAGCAGCUCCUGGUGGCGGGAGCUCACGAACUGCUGCACAGCGGCGGUGCUCGGAGGCGAGGCCACCGACGUGGUGGCGCC
..((((.....(((((..((((..((((((...((((....))))))))))(((((....)).)))...)))))))))..))))(((.((((....))))((((((.....))))))))) ( -56.70)
>DroYak_CAF1 1590 120 + 1
CAGCUGAUUGGGUGCAUAGUACAGCAGGGGAUACUGCGAGAGCAGCUCCUGGUGGCGGGAGCUCACGAACUGCUGCACUGCAGCGGUGCUCGGCGGCGAGGCCACCGAUGCAGUGGCGCC
..........(((((......((((((((((..((((....)))).)))).(((((....)).)))...))))))(((((((.(((((((((....))))..))))).)))))))))))) ( -60.20)
>DroAna_CAF1 24199 102 + 1
CAGCUGGUUGGGAGCGUAGUACAGCAGGGGAUACUGGGAAAGCAGCUCCUGGUGGCGGGUGUUUACAAAUUGCUGCACGGCUGUGG------------------CCGAGUUGGUGGCGCC
((((...(((..((((..((.((.((((((...(((......))))))))).))))...))))..)))...))))...(((.((.(------------------((.....))).))))) ( -34.80)
>consensus
CAGCUGAUUGGGUGCAUAGUACAGCAGGGGAUACUGCGAGAGCAGCUCCUGGUGGCGGGAGCUCACAAACUGCUGCACAGCAGCGGUGCUCGGCGGCGAGGCCACCGAUGUAGUGGCGCC
..........(((((......((((((((((..((((....)))).)))).(((((....)).)))...))))))(((.(((.(((((((((....))))..))))).))).)))))))) (-43.20 = -43.32 +   0.12)

alignment

secondary structure

dotplot

Window 0

Location	1,952,369 – 1,952,489
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.33
Mean single sequence MFE	-43.60
Consensus MFE	-32.97
Energy contribution	-34.98
Covariance contribution	2.00
Combinations/Pair	1.03
Mean z-score	-1.86
Structure conservation index	0.76
SVM decision value	0.67
SVM RNA-class probability	0.816500
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1952369 120 - 22407834
GGCGCCACUUCAUCGGUGGCCUCGCCGCCGAGCACCGCUGCUGUGCAGCAGUUUGUGAGCUCCCGCCACCAGGAGCUGCUCUCGCAGUAUCCCCUGCUGUACUAUGCACCCAAUCAGCUG
(((((.......((((((((...)))))))).....))(((.(((((((((...(((.((....)))))..((((((((....))))).))).)))))))))...)))........))). ( -48.90)
>DroEre_CAF1 4018 120 - 1
GGCGCCACCACGUCGGUGGCCUCGCCUCCGAGCACCGCCGCUGUGCAGCAGUUCGUGAGCUCCCGCCACCAGGAGCUGCUCUCGCAGUAUCCCCUGCUCUACUAUGCACCCAAUCAGCUG
(((((((((.....))))))((((....))))....)))((((((((((((((((((.((....)))))...)))))))....((((......)))).......)))))......))).. ( -46.70)
>DroYak_CAF1 1590 120 - 1
GGCGCCACUGCAUCGGUGGCCUCGCCGCCGAGCACCGCUGCAGUGCAGCAGUUCGUGAGCUCCCGCCACCAGGAGCUGCUCUCGCAGUAUCCCCUGCUGUACUAUGCACCCAAUCAGCUG
(((((...(((.((((((((...)))))))))))..))(((((((((((((...(((.((....)))))..((((((((....))))).))).)))))))))..))))........))). ( -53.40)
>DroAna_CAF1 24199 102 - 1
GGCGCCACCAACUCGG------------------CCACAGCCGUGCAGCAAUUUGUAAACACCCGCCACCAGGAGCUGCUUUCCCAGUAUCCCCUGCUGUACUACGCUCCCAACCAGCUG
((((((........))------------------)....)))((((((((...((....))..........(((((((......)))).)))..))))))))...(((.......))).. ( -25.40)
>consensus
GGCGCCACCACAUCGGUGGCCUCGCCGCCGAGCACCGCUGCUGUGCAGCAGUUCGUGAGCUCCCGCCACCAGGAGCUGCUCUCGCAGUAUCCCCUGCUGUACUAUGCACCCAAUCAGCUG
(((((((((.....))))))...................((.(((((((((...(((.((....)))))..((((((((....))))).))).)))))))))...)).........))). (-32.97 = -34.98 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:03 2006