Locus 7581

Sequence ID	3R_DroMel_CAF1
Location	20,317,649 – 20,317,744
Length	95
Max. P	0.912516

overview

Window 6

Location	20,317,649 – 20,317,744
Length	95
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	78.09
Mean single sequence MFE	-21.10
Consensus MFE	-9.72
Energy contribution	-11.20
Covariance contribution	1.48
Combinations/Pair	1.06
Mean z-score	-2.26
Structure conservation index	0.46
SVM decision value	1.08
SVM RNA-class probability	0.912516
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20317649 95 + 27905053
GCCGCAUCAAAGCAAAGGAGUAAACGAGCCCCAAG----GAUCUGGGCAAAAAAAAUACCAGAUCCAGACAGAAACCAUUUCUCAGCUUUUAACAUCUU
........(((((...((.((......)).))..(----(((((((............))))))))...................)))))......... ( -21.30)
>DroSec_CAF1 126402 93 + 1
GCCGCAUCAAAGCAAAGGAGUAAACGAGCCCCCAG----GAUCUGGGCAAA--AAAUACCAGAUCCAGCCAGAAACCAUUUCUCAGCUUUCCACAUCUU
...((......))...((((..............(----(((((((.....--.....))))))))(((.((((.....))))..)))))))....... ( -22.40)
>DroSim_CAF1 134833 93 + 1
GCCGCAUCAAAGCAAAGGAGUAAACGAGCCCCCAG----GAUCUGGGCAAA--AAAUACCAGAUCCAGCCAGAAACCAUUUCUCAGCUUUCCGCAUCUU
((.((......))...((((..............(----(((((((.....--.....))))))))(((.((((.....))))..)))))))))..... ( -24.00)
>DroEre_CAF1 129916 85 + 1
GCCGCAUCAAAGCAAAGGAGUAAACGAGCCCCAAG----GAUCUGG-CAAA--AAAUACCAGCUCCAGCCA--AACCAUUUCUCAGCUUUCGAG-----
......(((((((...((.((......)).))..(----((.((((-....--.....)))).))).....--............))))).)).----- ( -17.10)
>DroAna_CAF1 130791 86 + 1
ACCCCAUCAAAGGAAAGGAA-AAAGAAGCCCCAAGGCUGGAUCCGCCCUAUGUGGAAACCUAAUCCAGCCA-AAACAAUUUUUCACCA-----------
...........((....(((-((((......)..((((((((((((.....))))).......))))))).-......)))))).)).----------- ( -20.71)
>consensus
GCCGCAUCAAAGCAAAGGAGUAAACGAGCCCCAAG____GAUCUGGGCAAA__AAAUACCAGAUCCAGCCAGAAACCAUUUCUCAGCUUUCCACAUCUU
........(((((...((.((......)).)).......(((((((............)))))))....................)))))......... ( -9.72 = -11.20 +   1.48)

alignment

secondary structure

dotplot

Window 7

Location	20,317,649 – 20,317,744
Length	95
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	78.09
Mean single sequence MFE	-28.64
Consensus MFE	-15.42
Energy contribution	-16.70
Covariance contribution	1.28
Combinations/Pair	1.14
Mean z-score	-1.88
Structure conservation index	0.54
SVM decision value	0.30
SVM RNA-class probability	0.677832
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20317649 95 - 27905053
AAGAUGUUAAAAGCUGAGAAAUGGUUUCUGUCUGGAUCUGGUAUUUUUUUUGCCCAGAUC----CUUGGGGCUCGUUUACUCCUUUGCUUUGAUGCGGC
....(((..(((((.((((((((((..(.....((((((((((.......)).)))))))----)..)..)).))))).)))....)))))...))).. ( -29.80)
>DroSec_CAF1 126402 93 - 1
AAGAUGUGGAAAGCUGAGAAAUGGUUUCUGGCUGGAUCUGGUAUUU--UUUGCCCAGAUC----CUGGGGGCUCGUUUACUCCUUUGCUUUGAUGCGGC
....((((.(((((.((((((((((..((....((((((((((...--..)).)))))))----).))..)).))))).)))....)))))..)))).. ( -30.50)
>DroSim_CAF1 134833 93 - 1
AAGAUGCGGAAAGCUGAGAAAUGGUUUCUGGCUGGAUCUGGUAUUU--UUUGCCCAGAUC----CUGGGGGCUCGUUUACUCCUUUGCUUUGAUGCGGC
....((((.(((((.((((((((((..((....((((((((((...--..)).)))))))----).))..)).))))).)))....)))))..)))).. ( -33.10)
>DroEre_CAF1 129916 85 - 1
-----CUCGAAAGCUGAGAAAUGGUU--UGGCUGGAGCUGGUAUUU--UUUG-CCAGAUC----CUUGGGGCUCGUUUACUCCUUUGCUUUGAUGCGGC
-----.((.(((((.(((((((((((--(.(..(((.((((((...--..))-)))).))----).).)))).))))).)))....)))))))...... ( -25.70)
>DroAna_CAF1 130791 86 - 1
-----------UGGUGAAAAAUUGUUU-UGGCUGGAUUAGGUUUCCACAUAGGGCGGAUCCAGCCUUGGGGCUUCUUU-UUCCUUUCCUUUGAUGGGGU
-----------.((.((((((..((((-.(((((((((..((..((.....)))).)))))))))...))))...)))-))))).((((.....)))). ( -24.10)
>consensus
AAGAUGUGGAAAGCUGAGAAAUGGUUUCUGGCUGGAUCUGGUAUUU__UUUGCCCAGAUC____CUUGGGGCUCGUUUACUCCUUUGCUUUGAUGCGGC
.........(((((.(((((((((((((.((...(((((((((.......)).)))))))....)).))))).))))).)))....)))))........ (-15.42 = -16.70 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:25 2006