Locus 2281

Sequence ID	3R_DroMel_CAF1
Location	6,490,907 – 6,491,028
Length	121
Max. P	0.970104

overview

Window 8

Location	6,490,907 – 6,491,004
Length	97
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	80.57
Mean single sequence MFE	-36.47
Consensus MFE	-26.24
Energy contribution	-26.18
Covariance contribution	-0.05
Combinations/Pair	1.31
Mean z-score	-1.55
Structure conservation index	0.72
SVM decision value	0.46
SVM RNA-class probability	0.746260
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6490907 97 + 27905053
----AACCGGCCUAUAGCCGUCCCUUUUCAAAUAUGGCGAUGCCUGCCAUUGGCUGUUGCUCCACCAAAGGGGCGUGGCUGUGUGUCCACUUUGCUU-------------UUCG
----....(((.(((((((((((((((........(((((((((.......))).)))))).....))))))))..))))))).)))..........-------------.... ( -32.22)
>DroSec_CAF1 254503 97 + 1
----AACCGGCCUAUAGCCGUCCCUUUUCAAAUAUGGCGAUGCCUGCCAUUGGCUGUUGCUCCAACAAGAGGGCGUGGCUUUGCGGCCACUUUGCUU-------------UUGG
----....((((((.(((((((((((((.......(((((((((.......))).)))))).....))))))).)))))).)).)))).........-------------.... ( -32.80)
>DroSim_CAF1 283782 97 + 1
----AACCGGCCUAUAGCCGUCCCUUUUCAAAUAUGGCGAUGCCUGCCAUUGGCUGUUGCUCCACCAAGAGGGCGUGGCUUUGCAGCCACUUUGCUU-------------UUGG
----....(((..(((((((.............((((((.....))))))))))))).)))...(((((((.(.((((((....))))))..).)))-------------)))) ( -32.31)
>DroEre_CAF1 267616 95 + 1
-----ACCGGCCUAUAGCCGUCCCUUUUCAAAUAUGGCGAUGCCUGCCAUUGGCUGUUGCUCCAC-GAGGGGGCGUGGCCUUGCGGCCACUUUGCUU-------------UUGG
-----.(((((.....)))((((((((........(((((((((.......))).))))))....-))))))))((((((....)))))).......-------------..)) ( -36.70)
>DroYak_CAF1 263027 97 + 1
----AACCGGCCUAUAGCCGUCCCUUUUCAAAUAUGGCGACGCCUGCCAUUGGCCGUAGCUCCACCAAGGGGGCGUGGCCUUGCGGCCACUUUGCUU-------------UGGG
----..((((((.((.((((((((...........)).))))...)).)).))))((((((((......)))))((((((....))))))..)))..-------------.)). ( -39.20)
>DroPer_CAF1 265840 111 + 1
CGGCAGCCAGCAUACAGCCAUCUCUUUUCAAAUAUGGCGACUCAUCGCAUUGGCUGUUGCGGCCC-GAAGGGGCGUG-CCUACCGGUCGGUUGGAU-ACCGAUGCGCAUGCUGG
......((((((((((((((........((....))((((....))))..))))))).(((((((-....))))...-.......((((((.....-)))))).)))))))))) ( -45.60)
>consensus
____AACCGGCCUAUAGCCGUCCCUUUUCAAAUAUGGCGAUGCCUGCCAUUGGCUGUUGCUCCACCAAGGGGGCGUGGCCUUGCGGCCACUUUGCUU_____________UUGG
.......((((.....)))).(((((((.......(((((((((.......))).)))))).....))))))).((((((....))))))........................ (-26.24 = -26.18 +  -0.05)

alignment

secondary structure

dotplot

Window 9

Location	6,490,907 – 6,491,004
Length	97
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	80.57
Mean single sequence MFE	-36.78
Consensus MFE	-23.73
Energy contribution	-24.73
Covariance contribution	1.00
Combinations/Pair	1.21
Mean z-score	-2.06
Structure conservation index	0.65
SVM decision value	0.71
SVM RNA-class probability	0.830625
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6490907 97 - 27905053
CGAA-------------AAGCAAAGUGGACACACAGCCACGCCCCUUUGGUGGAGCAACAGCCAAUGGCAGGCAUCGCCAUAUUUGAAAAGGGACGGCUAUAGGCCGGUU----
....-------------.......((((........))))..((((((((((..((....(((...)))..))..)))))........))))).((((.....))))...---- ( -29.90)
>DroSec_CAF1 254503 97 - 1
CCAA-------------AAGCAAAGUGGCCGCAAAGCCACGCCCUCUUGUUGGAGCAACAGCCAAUGGCAGGCAUCGCCAUAUUUGAAAAGGGACGGCUAUAGGCCGGUU----
....-------------.....((.(((((....((((...((((...((((......))))..(((((.......)))))........))))..))))...))))).))---- ( -30.80)
>DroSim_CAF1 283782 97 - 1
CCAA-------------AAGCAAAGUGGCUGCAAAGCCACGCCCUCUUGGUGGAGCAACAGCCAAUGGCAGGCAUCGCCAUAUUUGAAAAGGGACGGCUAUAGGCCGGUU----
((..-------------...((((((((((....)))))).......(((((..((....(((...)))..))..)))))..)))).....)).((((.....))))...---- ( -34.50)
>DroEre_CAF1 267616 95 - 1
CCAA-------------AAGCAAAGUGGCCGCAAGGCCACGCCCCCUC-GUGGAGCAACAGCCAAUGGCAGGCAUCGCCAUAUUUGAAAAGGGACGGCUAUAGGCCGGU-----
((..-------------...((((((((((....))))))(((.((..-.(((........)))..))..))).........)))).....)).((((.....))))..----- ( -36.60)
>DroYak_CAF1 263027 97 - 1
CCCA-------------AAGCAAAGUGGCCGCAAGGCCACGCCCCCUUGGUGGAGCUACGGCCAAUGGCAGGCGUCGCCAUAUUUGAAAAGGGACGGCUAUAGGCCGGUU----
(((.-------------...((((((((((....)))))).......(((((..(((...(((...))).)))..)))))..))))....))).((((.....))))...---- ( -44.40)
>DroPer_CAF1 265840 111 - 1
CCAGCAUGCGCAUCGGU-AUCCAACCGACCGGUAGG-CACGCCCCUUC-GGGCCGCAACAGCCAAUGCGAUGAGUCGCCAUAUUUGAAAAGAGAUGGCUGUAUGCUGGCUGCCG
(((((((((((((((((-.....)))))..(((..(-(..((((....-)))).))....)))..)))........(((((.(((....))).))))).)))))))))...... ( -44.50)
>consensus
CCAA_____________AAGCAAAGUGGCCGCAAAGCCACGCCCCCUUGGUGGAGCAACAGCCAAUGGCAGGCAUCGCCAUAUUUGAAAAGGGACGGCUAUAGGCCGGUU____
........................((((((....))))))((((((((......((....))..(((((.......))))).......)))))..(((.....))))))..... (-23.73 = -24.73 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	6,490,937 – 6,491,028
Length	91
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	72.34
Mean single sequence MFE	-36.02
Consensus MFE	-21.58
Energy contribution	-22.47
Covariance contribution	0.89
Combinations/Pair	1.24
Mean z-score	-1.93
Structure conservation index	0.60
SVM decision value	1.65
SVM RNA-class probability	0.970104
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6490937 91 - 27905053
AUU-----------GCCCCCCC----AUUCAUUGGUG-GGCGAA-------------AAGCAAAGUGGACACACAGCCACGCCCCUUUGGUGGAGCAACAGCCAAUGGCAGGCAUCGCCA
.((-----------((((..((----(.....))).)-))))).-------------..((...(((....))).(((..(((...((((((......)).)))).))).)))...)).. ( -31.00)
>DroSec_CAF1 254533 91 - 1
AUU-----------GCCCCCCC----AUUCAUUGGUG-GGCCAA-------------AAGCAAAGUGGCCGCAAAGCCACGCCCUCUUGUUGGAGCAACAGCCAAUGGCAGGCAUCGCCA
..(-----------(((.((((----(.....))).)-)((((.-------------..((...(((((......)))))((((.......)).))....))...)))).))))...... ( -32.10)
>DroSim_CAF1 283812 91 - 1
AUU-----------GCCCCCCC----AUUCAUUGGUG-GGCCAA-------------AAGCAAAGUGGCUGCAAAGCCACGCCCUCUUGGUGGAGCAACAGCCAAUGGCAGGCAUCGCCA
..(-----------(((.((((----(.....))).)-)((((.-------------..((...((((((....))))))((((.......)).))....))...)))).))))...... ( -34.40)
>DroEre_CAF1 267645 97 - 1
--------UUUCAGGUUCCCCCCCCCCCCCAUUGGUU-GGCCAA-------------AAGCAAAGUGGCCGCAAGGCCACGCCCCCUC-GUGGAGCAACAGCCAAUGGCAGGCAUCGCCA
--------.....(((........((..(((((((((-(.(((.-------------.((....((((((....)))))).....)).-.))).....))))))))))..))....))). ( -39.30)
>DroYak_CAF1 263057 102 - 1
GUUUUGAGUUUGAGGUUCCCCC----AUUCAUUGGUU-GGCCCA-------------AAGCAAAGUGGCCGCAAGGCCACGCCCCCUUGGUGGAGCUACGGCCAAUGGCAGGCGUCGCCA
.............(((..(.((----..(((((((((-(((((.-------------.......((((((....))))))(((.....))))).))))..))))))))..)).)..))). ( -40.70)
>DroPer_CAF1 265874 102 - 1
CUC-----------GGCCCCCC----AUUCGUUGGCCGGGCCAGCAUGCGCAUCGGU-AUCCAACCGACCGGUAGG-CACGCCCCUUC-GGGCCGCAACAGCCAAUGCGAUGAGUCGCCA
...-----------(((..(.(----(((((((((((((....((....)).(((((-.....))))))))....(-(..((((....-)))).))....))))))).)))).)..))). ( -38.60)
>consensus
AUU___________GCCCCCCC____AUUCAUUGGUG_GGCCAA_____________AAGCAAAGUGGCCGCAAAGCCACGCCCCCUUGGUGGAGCAACAGCCAAUGGCAGGCAUCGCCA
............................((((((((............................((((((....))))))((.((......)).))....))))))))..(((...))). (-21.58 = -22.47 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:32 2006