Locus 635

Sequence ID	X_DroMel_CAF1
Location	1,764,960 – 1,765,065
Length	105
Max. P	0.962857

overview

Window 3

Location	1,764,960 – 1,765,065
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	67.26
Mean single sequence MFE	-35.90
Consensus MFE	-13.50
Energy contribution	-14.00
Covariance contribution	0.50
Combinations/Pair	1.31
Mean z-score	-2.24
Structure conservation index	0.38
SVM decision value	1.55
SVM RNA-class probability	0.962857
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1764960 105 + 22224390
AAAUUUUUUGGUCAGGGCUGUCGCCCCUCGCAUGGCA----------UCGAUAGAAGAGCGUCCGGAGCUGCGGUUGCAACCCUAUCCGCUCACGCAA-AUCUAUCGAAAAAUUUU----
(((((((...((((((((....))))......)))).----------((((((((...((((.((((...(.(((....))))..))))...))))..-.))))))))))))))).---- ( -32.40)
>DroSec_CAF1 6440 105 + 1
AAAUUUUUUGGUCAGGGUUGUCGGUCCUCGCAUGGCA----------UCGAUAGCAGAGCGUCCGGAGUUGCGGUUGCAACCCUGCCCGCUCACGCCA-ACCUAUCGAAAAAUUUU----
((((((((((((.((((((((((((((......)).)----------)))))))).(((((..(((.(((((....))))).)))..)))))......-.))))))))))))))).---- ( -44.70)
>DroEre_CAF1 6098 105 + 1
AAAUUUUUGGGCCAGGGCUGUCGCCCCUCGCAUGGCA----------UCGAUAGCAGAGCGCCCGAAGUUACGGUUGCAACCCUGUCCGCUCACGCAA-ACCUAUCGAAAAUUUUU----
(((((((((((.(((((((((((..((......))..----------.)))))))...(((.(((......))).)))...)))).))((....))..-......)))))))))..---- ( -34.00)
>DroWil_CAF1 8525 103 + 1
AAAGUU-CGCAUCAGGGUUGUCGUCCUACCUGCUGCACAUAGGUGCAA-GGUAUAA--UCGACUACG--AAUGGUGGCAAUCCUAC--------AUAAUAGUAAUCGAUAAUCAUAG---
......-...(((.(((((((((.(((((((..(((((....))))))-))))...--(((....))--)..)))))))))))(((--------......)))...)))........--- ( -27.80)
>DroYak_CAF1 6151 105 + 1
AAAUUUUUGGGCCAGGGCUGUCGCCUCUCGCAUGGCA----------UCGAUAUCAGAGCGCCCGGAGCUGCGGUUGCAACCCUGUCCGCUCACGCAA-ACCUAUCGAAAAUUUUU----
((((((((((...(((..(((.(((........))).----------.........(((((..(((.(.(((....))).).)))..)))))..))).-.))).))))))))))..---- ( -32.10)
>DroAna_CAF1 6238 114 + 1
AAAUUUAUAGGACAGGGUUGUCGCUGUUCGCACGGCAAAUGGCCGCUCCGAUAU----ACGGCCACGGCAGCAGUGGCAAUCCUGGCCACGGUCG-AA-ACCUAUCGAAAAUUUUUUUUU
((((((...((.((((((((((((((((.((.((.....((((((.........----.)))))))))))))))))))))))))).))....(((-(.-.....))))))))))...... ( -44.40)
>consensus
AAAUUUUUGGGUCAGGGCUGUCGCCCCUCGCAUGGCA__________UCGAUAGCAGAGCGCCCGGAGCUGCGGUUGCAACCCUGUCCGCUCACGCAA_ACCUAUCGAAAAUUUUU____
.........((.(((((.(((.(((........)))..........................(((......)))..))).))))).))................................ (-13.50 = -14.00 +   0.50)

alignment

secondary structure

dotplot

Window 4

Location	1,764,960 – 1,765,065
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	67.26
Mean single sequence MFE	-34.85
Consensus MFE	-15.36
Energy contribution	-15.98
Covariance contribution	0.62
Combinations/Pair	1.32
Mean z-score	-1.69
Structure conservation index	0.44
SVM decision value	0.51
SVM RNA-class probability	0.764621
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1764960 105 - 22224390
----AAAAUUUUUCGAUAGAU-UUGCGUGAGCGGAUAGGGUUGCAACCGCAGCUCCGGACGCUCUUCUAUCGA----------UGCCAUGCGAGGGGCGACAGCCCUGACCAAAAAAUUU
----.(((((((((((((((.-......(((((..(.(((((((....))))))).)..))))).))))))))----------.....((...(((((....)))))...)).))))))) ( -38.70)
>DroSec_CAF1 6440 105 - 1
----AAAAUUUUUCGAUAGGU-UGGCGUGAGCGGGCAGGGUUGCAACCGCAACUCCGGACGCUCUGCUAUCGA----------UGCCAUGCGAGGACCGACAACCCUGACCAAAAAAUUU
----.((((((((.(...(((-(((((.(((((..(.(((((((....))))))).)..))))))))..(((.----------..((......))..)))))))).....).)))))))) ( -34.10)
>DroEre_CAF1 6098 105 - 1
----AAAAAUUUUCGAUAGGU-UUGCGUGAGCGGACAGGGUUGCAACCGUAACUUCGGGCGCUCUGCUAUCGA----------UGCCAUGCGAGGGGCGACAGCCCUGGCCCAAAAAUUU
----........(((((((((-((((....))))))(((((.((..(((......)))))))))).)))))))----------......((..(((((....))))).)).......... ( -39.00)
>DroWil_CAF1 8525 103 - 1
---CUAUGAUUAUCGAUUACUAUUAU--------GUAGGAUUGCCACCAUU--CGUAGUCGA--UUAUACC-UUGCACCUAUGUGCAGCAGGUAGGACGACAACCCUGAUGCG-AACUUU
---.....((.(((((((((....((--------(..((....))..))).--.))))))))--).))...-.(((((....)))))(((..((((........)))).))).-...... ( -25.50)
>DroYak_CAF1 6151 105 - 1
----AAAAAUUUUCGAUAGGU-UUGCGUGAGCGGACAGGGUUGCAACCGCAGCUCCGGGCGCUCUGAUAUCGA----------UGCCAUGCGAGAGGCGACAGCCCUGGCCCAAAAAUUU
----..(((((((........-..((....))((.((((((((....(((..(((((((((.((.......))----------)))).)).)))..))).))))))))..)).))))))) ( -36.60)
>DroAna_CAF1 6238 114 - 1
AAAAAAAAAUUUUCGAUAGGU-UU-CGACCGUGGCCAGGAUUGCCACUGCUGCCGUGGCCGU----AUAUCGGAGCGGCCAUUUGCCGUGCGAACAGCGACAACCCUGUCCUAUAAAUUU
......((((((..((((((.-..-.....(((((.......)))))(((((..((((((((----........))))))))((((...)))).))))).....))))))....)))))) ( -35.20)
>consensus
____AAAAAUUUUCGAUAGGU_UUGCGUGAGCGGACAGGGUUGCAACCGCAGCUCCGGACGCUCUGAUAUCGA__________UGCCAUGCGAGGGGCGACAACCCUGACCCAAAAAUUU
........................((....))((.(((((((((..(((......))).(((...........................)))......).)))))))).))......... (-15.36 = -15.98 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:56 2006