Locus 5697

Sequence ID	2R_DroMel_CAF1
Location	18,042,535 – 18,042,741
Length	206
Max. P	0.656487

overview

Window 3

Location	18,042,535 – 18,042,638
Length	103
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	78.71
Mean single sequence MFE	-35.59
Consensus MFE	-24.08
Energy contribution	-27.00
Covariance contribution	2.92
Combinations/Pair	1.14
Mean z-score	-1.23
Structure conservation index	0.68
SVM decision value	0.14
SVM RNA-class probability	0.602363
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18042535 103 + 20766785
CAGAUUGCAUUGUC----CAGCUACUGAAAUACACA-GAUACUCACAAUGCGAUCGGAGCGCUCGCCGCAGGGCAAGCGGGCCACUGCGGACUCGGGACUGUCCUCUG
..(((((((((((.----.((.(((((.......))-).)))).)))))))))))(((...(((((((((((((......))).))))))...))))....))).... ( -38.70)
>DroVir_CAF1 155 88 + 1
---U-----------------CUAUUGGCAUAAACAGUUUACUCACAAUACGAUCGGAGCGUUCGCCGCAGGGCAAACGCGCCACUGCGGCAUCGGGGCUGUCCUCCG
---(-----------------((((((..................))))).)).(((((.((((((((((((((......))).)))))))....))))....))))) ( -28.37)
>DroSim_CAF1 114 103 + 1
CAGAUUGCAUUGUC----CAGCUACUGGAAUACACC-GAUACUCACAAUGCGAUCGGAGCGCUCGCCGCAGGGCAAGCGGGCCACUGCGGACUCGGGACUGUCCUCCG
..((((((((((((----(((...))))).......-(.....).))))))))))((((..(((((((((((((......))).))))))...))))......)))). ( -42.30)
>DroEre_CAF1 115 103 + 1
CAGAUUGCAUUGUC----CAGCUACUGGAAUACUCA-GAUACUCACAAUGCGAUCGGAGCGCUCGCCGCAGGGCAAGCGGGCCACUGCGGACUCGGGACUGUCCUCCG
..((((((((((((----(((...))))).......-(.....).))))))))))((((..(((((((((((((......))).))))))...))))......)))). ( -42.20)
>DroWil_CAF1 36158 88 + 1
CAGGUUA-------------------GUAAUGGAGA-GUUACUCACAAUACGAUCAGAGCGUUCGCCGCAGGGCAAACGUGCUACUGCCGAUUCGGGACUAUCCUCGG
.(((.((-------------------((..((((((-(...)))......((..(((.(((((.(((....))).)))))....))).)).))))..)))).)))... ( -23.00)
>DroYak_CAF1 116 108 + 1
CAGAUUGCAUUGUAUCUGGAGCUACUGGAAUACACAAAAUACUCACAAUGCGAUCGGUGCGCUCGCCGCAGGGCAAGCGGGCCACUGCGGACUCGGGACUGUCCUCCG
..(((((((((((.....(((....((.......)).....))))))))))))))(((.((((.(((....))).)))).))).....((((........)))).... ( -39.00)
>consensus
CAGAUUGCAUUGUC____CAGCUACUGGAAUACACA_GAUACUCACAAUGCGAUCGGAGCGCUCGCCGCAGGGCAAGCGGGCCACUGCGGACUCGGGACUGUCCUCCG
..(((((((((((...............................)))))))))))((((..(((((((((((((......))).))))))...))))......)))). (-24.08 = -27.00 +   2.92)

alignment

secondary structure

dotplot

Window 4

Location	18,042,638 – 18,042,741
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.81
Mean single sequence MFE	-41.38
Consensus MFE	-29.42
Energy contribution	-29.17
Covariance contribution	-0.25
Combinations/Pair	1.22
Mean z-score	-1.01
Structure conservation index	0.71
SVM decision value	0.26
SVM RNA-class probability	0.655671
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18042638 103 + 20766785
GCGGAGGCGGUUGGGGCACCCAGUUGUAGGCCCGCCUGGAUAUGGGCACUCCAAAGCGAUCGUGCUGUGAGGCUUGUUGUCUGCAAA-GA--------------AAACAU-U-AAUUAUU
((((..((..((((((..((((..(.((((....)))).)..))))..)))))).))..))))(((....))).((((.(((....)-))--------------.)))).-.-....... ( -32.00)
>DroPse_CAF1 337 114 + 1
GGGGCGGCGGCUGGGGCACCCAAUUGUAGGCCCGCCUAGAUAUGGGCACCCCGAAGCGGUCGUGCUGCGAGGCCUGUUGUCUGUGGAAGGAAAC---A---AGCACACGUCUCAGUUAGU
((.(((((.(((((((..((((..(.((((....)))).)..))))..))))..))).))))).))..(((((.(((.(..(((........))---)---..)))).)))))....... ( -47.90)
>DroWil_CAF1 36246 99 + 1
GCGGCGGCGGUUGGGGUACCCAAUUGUAGGCCCGCCUCGAUAUAGGCACCCCAAAUCGAUCGUGCUGCGAUGCUUGUUGUCUGCAAUAGGAGAU------------CCUU-U--------
((((((.((((((((((.((..((((.(((....)))))))...)).))))).)))))....))))))(((.(((((((....)))))))..))------------)...-.-------- ( -38.60)
>DroMoj_CAF1 212 111 + 1
GUGGCGGCGGCUGGGGCACCCAGUUGUAGGCCCGCCUAGAGAUGGGCACCCCAAAGCGAUCAUGCUGCGACGCCUGUUGCCUGUGAA--AGUGGAAGUGGAAA---GAAU-U-AGUUA--
..((((((((((((((..((((.((.((((....)))).)).))))..))))).(((......))).....))).))))))......--..............---....-.-.....-- ( -39.10)
>DroAna_CAF1 219 112 + 1
GGGGCGGCGGCUGGGGCACCCAGUUGUAGGCCCGCCUCGAUAUGGGCACCCCGAAGCGAUCAUGCUGCGAGGCUUGUUGUCUGCAAA-AA-UAU---U---GGAACAGAUGUCAAUUAGU
.((((.(((((((((...)))))))))..))))((((((...((((...)))).(((......))).))))))(((.(((((((((.-..-..)---)---)...)))))).)))..... ( -42.80)
>DroPer_CAF1 338 114 + 1
GGGGCGGCGGCUGGGGCACCCAAUUGUAGGCCCGCCUAGAUAUGGGCACCCCGAAGCGGUCGUGCUGCGAGGCCUGUUGUCUGUGAAAGGAAAC---A---AGCACACGUCUCAGUUAGU
((.(((((.(((((((..((((..(.((((....)))).)..))))..))))..))).))))).))..(((((.(((.(..(((........))---)---..)))).)))))....... ( -47.90)
>consensus
GGGGCGGCGGCUGGGGCACCCAAUUGUAGGCCCGCCUAGAUAUGGGCACCCCAAAGCGAUCGUGCUGCGAGGCCUGUUGUCUGCAAA_GAAAAC_______AG_ACACAU_U_AGUUAGU
..((((((((((((((..((((..(.((((....)))).)..))))..))))).((((....)))).....))).))))))....................................... (-29.42 = -29.17 +  -0.25)

alignment

secondary structure

dotplot

Window 5

Location	18,042,638 – 18,042,741
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.81
Mean single sequence MFE	-34.88
Consensus MFE	-25.06
Energy contribution	-25.03
Covariance contribution	-0.03
Combinations/Pair	1.16
Mean z-score	-0.98
Structure conservation index	0.72
SVM decision value	0.26
SVM RNA-class probability	0.656487
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18042638 103 - 20766785
AAUAAUU-A-AUGUUU--------------UC-UUUGCAGACAACAAGCCUCACAGCACGAUCGCUUUGGAGUGCCCAUAUCCAGGCGGGCCUACAACUGGGUGCCCCAACCGCCUCCGC
.......-.-.((((.--------------((-(....))).)))).(((((..(((......)))...))).))........(((((((((((....))))).......)))))).... ( -24.01)
>DroPse_CAF1 337 114 - 1
ACUAACUGAGACGUGUGCU---U---GUUUCCUUCCACAGACAACAGGCCUCGCAGCACGACCGCUUCGGGGUGCCCAUAUCUAGGCGGGCCUACAAUUGGGUGCCCCAGCCGCCGCCCC
.....(((.((.((.((.(---(---((((........)))))))).)).)).)))..((.(.(((..((((..((((....((((....))))....))))..))))))).).)).... ( -40.20)
>DroWil_CAF1 36246 99 - 1
--------A-AAGG------------AUCUCCUAUUGCAGACAACAAGCAUCGCAGCACGAUCGAUUUGGGGUGCCUAUAUCGAGGCGGGCCUACAAUUGGGUACCCCAACCGCCGCCGC
--------.-.(((------------....)))..(((.........)))..((.((.(....)..((((((((((((.....(((....))).....))))))))))))..)).))... ( -31.50)
>DroMoj_CAF1 212 111 - 1
--UAACU-A-AUUC---UUUCCACUUCCACU--UUCACAGGCAACAGGCGUCGCAGCAUGAUCGCUUUGGGGUGCCCAUCUCUAGGCGGGCCUACAACUGGGUGCCCCAGCCGCCGCCAC
--.....-.-....---..............--......(((....((((..(((((......))).(((((..((((....((((....))))....))))..)))))))))))))).. ( -39.40)
>DroAna_CAF1 219 112 - 1
ACUAAUUGACAUCUGUUCC---A---AUA-UU-UUUGCAGACAACAAGCCUCGCAGCAUGAUCGCUUCGGGGUGCCCAUAUCGAGGCGGGCCUACAACUGGGUGCCCCAGCCGCCGCCCC
.....(((...(((((...---.---...-..-...)))))...)))((...((.((..((.....))((((..((((.....(((....))).....))))..)))).)).)).))... ( -34.00)
>DroPer_CAF1 338 114 - 1
ACUAACUGAGACGUGUGCU---U---GUUUCCUUUCACAGACAACAGGCCUCGCAGCACGACCGCUUCGGGGUGCCCAUAUCUAGGCGGGCCUACAAUUGGGUGCCCCAGCCGCCGCCCC
.....(((.((.((.((.(---(---((((........)))))))).)).)).)))..((.(.(((..((((..((((....((((....))))....))))..))))))).).)).... ( -40.20)
>consensus
ACUAACU_A_AUGUGU_CU_______AUAUCC_UUCACAGACAACAAGCCUCGCAGCACGAUCGCUUCGGGGUGCCCAUAUCUAGGCGGGCCUACAACUGGGUGCCCCAGCCGCCGCCCC
....................................................((.((..((.....))((((((((((.....(((....))).....))))))))))....)).))... (-25.06 = -25.03 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:06 2006