Locus 6338

Sequence ID	3R_DroMel_CAF1
Location	16,587,779 – 16,587,881
Length	102
Max. P	0.850149

overview

Window 5

Location	16,587,779 – 16,587,881
Length	102
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	79.32
Mean single sequence MFE	-35.92
Consensus MFE	-20.75
Energy contribution	-21.33
Covariance contribution	0.59
Combinations/Pair	1.10
Mean z-score	-2.01
Structure conservation index	0.58
SVM decision value	0.59
SVM RNA-class probability	0.790599
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16587779 102 + 27905053
GGCCUGCCACUCGUGUUGGGCGAACACGCCCACGGCGAGCACCAGCAUAAAAAGCAAAUAGCUGCGCCCCAAAAUCGACGACGG---GAACAUUUUG---------CCCGACUC
((((((...(((((..((((((....))))))..)))))...)))........(((......)))))).............(((---(.........---------)))).... ( -31.90)
>DroVir_CAF1 172570 108 + 1
CGCCUGCCACUCGUGCUGGGCGAACACGCCCACGACCAGCGCCAGCACAAAAAGCAGGUAGCUGCGCCCCAAAAUCGUUGACGGCAGAAACAA---AACCAUGUU---UGUUUG
...(((((....((((((((((....))))).((.....))..))))).....((((....)))).................)))))((((((---(......))---))))). ( -34.70)
>DroPse_CAF1 146239 111 + 1
AGCCUGCCACUCGUGCUGGGCGAACACGCCCACGGCGAGUACCAGCAUAAAAAGCAGGUAGCUGCGCCCCAAAAUCGUCGAGGG---AAACAUUCUAGUUAUGUUUUCUGGCUA
((((.....((((.((((((((....)))))).((((((((((.((.......)).))).))).))))........))))))((---((((((.......)))))))).)))). ( -41.60)
>DroWil_CAF1 165898 101 + 1
AGCCUGCCACUCAUGCUGAGCUAACACACCCACAGUCAGCACCAGCAUGAAAAGCAGAUAGCUGCGCCCUAAAAUAGUCGAAGG---AAACAUUUUG---------UCCC-UUC
(((((((...((((((((.(((.((.........)).)))..))))))))...))))...)))................(((((---..((.....)---------).))-))) ( -25.90)
>DroAna_CAF1 141395 100 + 1
GGCCUGCCACUCGUGCUGGGCGAACACGCCCACGGCGAGCACCAGCAUAAAAAGCAGGUAGCUGCGCCCCAAAAUCGUCGAGGG---GAACAUUUUG---------U--AGCUG
.((((((.....(((((((((.....((((...)))).)).))))))).....))))))(((((((((((...........)))---).......))---------)--)))). ( -41.21)
>DroPer_CAF1 153594 111 + 1
GGCCUGCCACUCGUGCUGGGCGAACACGCCCACGGCGAGUACCAGCAUAAAAAGCAGGUAGCUGCGCCCCAAAAUCGUCGAGGG---AAACAUUCUAGUUAUGCUUUCUGGCUA
((((....((((((..((((((....))))))..))))))...(((((((...((((....))))..(((...........)))---...........)))))))....)))). ( -40.20)
>consensus
GGCCUGCCACUCGUGCUGGGCGAACACGCCCACGGCGAGCACCAGCAUAAAAAGCAGGUAGCUGCGCCCCAAAAUCGUCGAGGG___AAACAUUUUA_________UCUGGCUA
.(((((...(((((..((((((....))))))..)))))...)))........((((....))))))............................................... (-20.75 = -21.33 +   0.59)

alignment

secondary structure

dotplot

Window 6

Location	16,587,779 – 16,587,881
Length	102
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.32
Mean single sequence MFE	-40.37
Consensus MFE	-28.58
Energy contribution	-28.03
Covariance contribution	-0.55
Combinations/Pair	1.32
Mean z-score	-1.67
Structure conservation index	0.71
SVM decision value	0.78
SVM RNA-class probability	0.850149
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16587779 102 - 27905053
GAGUCGGG---------CAAAAUGUUC---CCGUCGUCGAUUUUGGGGCGCAGCUAUUUGCUUUUUAUGCUGGUGCUCGCCGUGGGCGUGUUCGCCCAACACGAGUGGCAGGCC
(((.((((---------.((....)))---))).).))........(((((((....))))........(((.((((((...((((((....))))))...)))))).)))))) ( -36.90)
>DroVir_CAF1 172570 108 - 1
CAAACA---AACAUGGUU---UUGUUUCUGCCGUCAACGAUUUUGGGGCGCAGCUACCUGCUUUUUGUGCUGGCGCUGGUCGUGGGCGUGUUCGCCCAGCACGAGUGGCAGGCG
.(((((---((......)---))))))(((((.((((.....)))).).))))...((((((.(((((((((((....)))..(((((....))))))))))))).)))))).. ( -43.20)
>DroPse_CAF1 146239 111 - 1
UAGCCAGAAAACAUAACUAGAAUGUUU---CCCUCGACGAUUUUGGGGCGCAGCUACCUGCUUUUUAUGCUGGUACUCGCCGUGGGCGUGUUCGCCCAGCACGAGUGGCAGGCU
.((((...((((((.......))))))---((((((..........((((.((.((((.((.......)).)))))))))).((((((....))))))...)))).))..)))) ( -41.40)
>DroWil_CAF1 165898 101 - 1
GAA-GGGA---------CAAAAUGUUU---CCUUCGACUAUUUUAGGGCGCAGCUAUCUGCUUUUCAUGCUGGUGCUGACUGUGGGUGUGUUAGCUCAGCAUGAGUGGCAGGCU
(((-((((---------........))---)))))...........(((...))).((((((.((((((((((.((((((.........)))))))))))))))).)))))).. ( -39.30)
>DroAna_CAF1 141395 100 - 1
CAGCU--A---------CAAAAUGUUC---CCCUCGACGAUUUUGGGGCGCAGCUACCUGCUUUUUAUGCUGGUGCUCGCCGUGGGCGUGUUCGCCCAGCACGAGUGGCAGGCC
.((((--.---------......((.(---(((...........)))).)))))).((((((.((..(((((((....)))..(((((....)))))))))..)).)))))).. ( -39.41)
>DroPer_CAF1 153594 111 - 1
UAGCCAGAAAGCAUAACUAGAAUGUUU---CCCUCGACGAUUUUGGGGCGCAGCUACCUGCUUUUUAUGCUGGUACUCGCCGUGGGCGUGUUCGCCCAGCACGAGUGGCAGGCC
..(((....(((((((((((((((((.---.....))).)))))))...((((....))))...)))))))(.((((((...((((((....))))))...)))))).).))). ( -42.00)
>consensus
CAGCCAGA_________CAAAAUGUUU___CCCUCGACGAUUUUGGGGCGCAGCUACCUGCUUUUUAUGCUGGUGCUCGCCGUGGGCGUGUUCGCCCAGCACGAGUGGCAGGCC
..............................................(((((((....))))........(((.((((((...((((((....))))))...)))))).)))))) (-28.58 = -28.03 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:03 2006