Locus 3892

Sequence ID	3L_DroMel_CAF1
Location	11,267,818 – 11,267,928
Length	110
Max. P	0.938978

overview

Window 0

Location	11,267,818 – 11,267,911
Length	93
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	85.61
Mean single sequence MFE	-46.63
Consensus MFE	-36.40
Energy contribution	-35.52
Covariance contribution	-0.88
Combinations/Pair	1.29
Mean z-score	-1.87
Structure conservation index	0.78
SVM decision value	0.02
SVM RNA-class probability	0.542463
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11267818 93 - 23771897
CUUACCGCUCGCAUUGCGGCCACUGUGGCCGCCGUUGCUGCCGCUGCGGCUGCAGCAAACGCUCGAGAUCGGGAGC------GGGAUGUGGAUACCGCU
....((((((((...((((((.....))))))..(((((((.((....)).)))))))..))(((....)))))))------))...((((...)))). ( -44.80)
>DroSec_CAF1 6117 93 - 1
CUUACCGCUCGUAUUGCGGCCACUGUGGCCGCCGUUGCUGCCGCUGCGGCGGCUGCAAACGCUCGAGAUCGGGAGC------GGGAUGUGGAUACCGCU
....((((((.(((..((((...((..((((((((.((....)).))))))))..))...)).))..)).).))))------))...((((...)))). ( -45.60)
>DroSim_CAF1 2496 93 - 1
CUUACCGCUCGUAUUGCGGCCACUGUGGCCGCCGUUGCUGCCGCUGCGGCGGCUGCCAACGCUCGAGAUCGGGAGC------GGGAUGUGGAUACCGCU
....((((((.....((((((.....))))))((((((.(((((....))))).).))))).(((....)))))))------))...((((...)))). ( -44.60)
>DroEre_CAF1 22947 93 - 1
CUUACCGCUCGCAUCGCGGCCACUGUGGCCGCCGUUGCUGCCGCUGCGGCGGCUGCAAACGCUCGAGAUCGGGAGC------GAGAUGUGGACACCGCU
......(..((((((((((((.....))))))..((((.(((((....))))).)))).(((((........))))------).))))))..)...... ( -46.10)
>DroYak_CAF1 2897 93 - 1
CUUACCGCUCGCAUUGCGGCCACUGUGGCCGCCGUUGCUGCCGCAGCAGCGGUUGCAAAUGCUCGAGAUCGGGAGC------GGGAUGUGGAUACCGCU
....(((((((((((((((((.....))))((((((((((...)))))))))).)).)))))(((....)))))))------))...((((...)))). ( -47.20)
>DroAna_CAF1 2527 99 - 1
CUGGCCGCCCGCUUUGCCGCUACAGUGGCGGCUGUGGCAGCUGCCGCUGCUGCCGCCAAUGCCAGGGAUCGGGAGCGGGAGCGAGAAGCGGACACCGCC
((.((..(((((((((((((....)))))(((.((((((((.......))))))))....)))........)))))))).)).))..((((...)))). ( -51.50)
>consensus
CUUACCGCUCGCAUUGCGGCCACUGUGGCCGCCGUUGCUGCCGCUGCGGCGGCUGCAAACGCUCGAGAUCGGGAGC______GGGAUGUGGAUACCGCU
....(((((((....((((((.....))))))((((((.(((((....))))).))).)))..))))..)))...............((((...)))). (-36.40 = -35.52 +  -0.88)

alignment

secondary structure

dotplot

Window 1

Location	11,267,837 – 11,267,928
Length	91
Sequences	6
Columns	91
Reading direction	forward
Mean pairwise identity	79.93
Mean single sequence MFE	-42.55
Consensus MFE	-30.60
Energy contribution	-32.30
Covariance contribution	1.70
Combinations/Pair	1.28
Mean z-score	-1.89
Structure conservation index	0.72
SVM decision value	0.93
SVM RNA-class probability	0.883270
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11267837 91 + 23771897
UCCCGAUCUCGAGCGUUUGCUGCAGCCGCAGCGGCAGCAACGGCGGCCACAGUGGCCGCAAUGCGAGCGGUAAGCUCAUCGUGUUGCUGCU
...((....)).......(((((....)))))((((((((((((((((.....)))))).....((((.....))))....)))))))))) ( -44.50)
>DroSim_CAF1 2515 91 + 1
UCCCGAUCUCGAGCGUUGGCAGCCGCCGCAGCGGCAGCAACGGCGGCCACAGUGGCCGCAAUACGAGCGGUAAGCUCAUCGUGUUGCUGCU
...((....)).((..((((....))))..))((((((((((((((((.....)))))).....((((.....))))....)))))))))) ( -43.50)
>DroEre_CAF1 22966 91 + 1
UCCCGAUCUCGAGCGUUUGCAGCCGCCGCAGCGGCAGCAACGGCGGCCACAGUGGCCGCGAUGCGAGCGGUAAGCUCGUCGUGUUGCUGCU
...((....))(((.......(((((....)))))((((((.((((((.....)))))).((((((((.....))))).)))))))))))) ( -44.50)
>DroYak_CAF1 2916 91 + 1
UCCCGAUCUCGAGCAUUUGCAACCGCUGCUGCGGCAGCAACGGCGGCCACAGUGGCCGCAAUGCGAGCGGUAAGCUCAUCGUGUUGCUGCU
...((....))((((...((....))))))(((((((((.((((((((.....)))))).....((((.....))))..))))))))))). ( -40.70)
>DroMoj_CAF1 1893 91 + 1
UCCCGUUCCCUGACGUUCGCCGCGGCUGCGGCUGCAGCCACAACAGCAACGGCGGCAGCGACGCGAGCAGCGAAGUCUUCGUGCUGCUCAG
.............((((.(((((((((((....))))))....(......))))))))))....((((((((.........)))))))).. ( -37.50)
>DroAna_CAF1 2552 91 + 1
UCCCGAUCCCUGGCAUUGGCGGCAGCAGCGGCAGCUGCCACAGCCGCCACUGUAGCGGCAAAGCGGGCGGCCAGCUCCUCGUGCUGCUGCU
............(((.(((((((.(((((....)))))....))))))).)))(((((((..(((((.((....)).)))))..))))))) ( -44.60)
>consensus
UCCCGAUCUCGAGCGUUUGCAGCCGCCGCAGCGGCAGCAACGGCGGCCACAGUGGCCGCAAUGCGAGCGGUAAGCUCAUCGUGUUGCUGCU
..................(((((....)))))((((((((((((((((.....)))))).....((((.....))))....)))))))))) (-30.60 = -32.30 +   1.70)

alignment

secondary structure

dotplot

Window 2

Location	11,267,837 – 11,267,928
Length	91
Sequences	6
Columns	91
Reading direction	reverse
Mean pairwise identity	79.93
Mean single sequence MFE	-44.18
Consensus MFE	-34.01
Energy contribution	-34.85
Covariance contribution	0.84
Combinations/Pair	1.37
Mean z-score	-2.26
Structure conservation index	0.77
SVM decision value	1.30
SVM RNA-class probability	0.938978
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11267837 91 - 23771897
AGCAGCAACACGAUGAGCUUACCGCUCGCAUUGCGGCCACUGUGGCCGCCGUUGCUGCCGCUGCGGCUGCAGCAAACGCUCGAGAUCGGGA
.((((((((..(.(((((.....))))))...((((((.....)))))).)))))))).(((((....))))).....((((....)))). ( -45.50)
>DroSim_CAF1 2515 91 - 1
AGCAGCAACACGAUGAGCUUACCGCUCGUAUUGCGGCCACUGUGGCCGCCGUUGCUGCCGCUGCGGCGGCUGCCAACGCUCGAGAUCGGGA
.((((((((...((((((.....))))))...((((((.....)))))).))))))(((((....))))).)).....((((....)))). ( -43.70)
>DroEre_CAF1 22966 91 - 1
AGCAGCAACACGACGAGCUUACCGCUCGCAUCGCGGCCACUGUGGCCGCCGUUGCUGCCGCUGCGGCGGCUGCAAACGCUCGAGAUCGGGA
.((((((((..(.(((((.....))))))...((((((.....)))))).))))))(((((....))))).)).....((((....)))). ( -45.50)
>DroYak_CAF1 2916 91 - 1
AGCAGCAACACGAUGAGCUUACCGCUCGCAUUGCGGCCACUGUGGCCGCCGUUGCUGCCGCAGCAGCGGUUGCAAAUGCUCGAGAUCGGGA
.((((((((..(.(((((.....))))))...((((((.....)))))).)))))))).(((((....))))).....((((....)))). ( -43.40)
>DroMoj_CAF1 1893 91 - 1
CUGAGCAGCACGAAGACUUCGCUGCUCGCGUCGCUGCCGCCGUUGCUGUUGUGGCUGCAGCCGCAGCCGCGGCGAACGUCAGGGAACGGGA
..(((((((...........))))))).((((.(((.((.((((((.((((((((....)))))))).))))))..)).))).).)))... ( -44.10)
>DroAna_CAF1 2552 91 - 1
AGCAGCAGCACGAGGAGCUGGCCGCCCGCUUUGCCGCUACAGUGGCGGCUGUGGCAGCUGCCGCUGCUGCCGCCAAUGCCAGGGAUCGGGA
.((((((((....(((((((.((((..(((..(((((....)))))))).))))))))).))))))))))..((....(....)....)). ( -42.90)
>consensus
AGCAGCAACACGAUGAGCUUACCGCUCGCAUUGCGGCCACUGUGGCCGCCGUUGCUGCCGCUGCGGCGGCUGCAAACGCUCGAGAUCGGGA
.((((((((.....((((.....)))).....((((((.....)))))).)))))))).(((((....))))).....((((....)))). (-34.01 = -34.85 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:22 2006