Locus 7157

Sequence ID	3R_DroMel_CAF1
Location	18,867,026 – 18,867,201
Length	175
Max. P	0.683621

overview

Window 7

Location	18,867,026 – 18,867,134
Length	108
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	82.11
Mean single sequence MFE	-28.68
Consensus MFE	-15.74
Energy contribution	-17.20
Covariance contribution	1.46
Combinations/Pair	1.10
Mean z-score	-2.15
Structure conservation index	0.55
SVM decision value	0.29
SVM RNA-class probability	0.671737
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18867026 108 + 27905053
CCGGCCGAUUGGCU--CAAUUUGCAUGCAAUUAAAAAUAAAUUGAGGCACCUUGUUCUGCGGCUAAACUAAAUAGUGGCACCGCAUUCGGUGGAGCCCACUUCCAAUUUU--
..(((((...((..--(((..(((...(((((.......)))))..)))..)))..)).))))).........((((((.((((.....)))).).))))).........-- ( -28.70)
>DroSec_CAF1 91905 108 + 1
CCGACCGAUUGGCUUUCAAUUUGCAUUCAAUUAAAAAUAAAUUGAGGCACCUUGUUCUGCGGCUA-ACUAAAUAGUGGCACCGCAUUCGGUGGAGCCCACU-CCAAUUUU--
...(((((...((...(((..(((.(((((((.......))))))))))..)))...(((.((((-......)))).)))..))..)))))((((....))-))......-- ( -30.30)
>DroEre_CAF1 94269 102 + 1
----CCGAUUGGCU--CAAUUUGCAUUCAAUUAAAAAUAAAUUGAGGCACCUUGUUCUGCGGCUA-ACUAAAUAGUGGCACCGCACUCGGUGCAACCCACU-CCAAUUUU--
----..((((((((--(((((((..............)))))))))(((((.(((..(((.((((-......)))).)))..)))...)))))........-))))))..-- ( -29.34)
>DroYak_CAF1 98597 108 + 1
GCGGCCGAUUGGCU--CAAUUUGCAUUCAAUUAAAAAUAAAUUGAGGCACCUUGUUCUGCGGCUA-ACUAAAUAGUGGCAUCGCACUCGGUGGAGCCCACU-CCAAUUUUUU
...(((((.((.((--(((((((..............))))))))).))...(((..(((.((((-......)))).)))..))).)))))((((....))-))........ ( -30.44)
>DroAna_CAF1 95564 94 + 1
CUCGGCGAUUGCCU--UAAUUUGCCUUCAAUUAAAAAUAAAUUGAGGCACCUUGUUUUGUGGCAA-GCUAAAUAG--------------GAGGAGCUCGCU-UCACUCAGUU
...(((((...(((--(....(((((.(((((.......)))))))))).((((((....)))))-)........--------------))))...)))))-.......... ( -24.60)
>consensus
CCGGCCGAUUGGCU__CAAUUUGCAUUCAAUUAAAAAUAAAUUGAGGCACCUUGUUCUGCGGCUA_ACUAAAUAGUGGCACCGCACUCGGUGGAGCCCACU_CCAAUUUU__
......(((((((...(((..(((.(((((((.......))))))))))..)))....)).............((((((((((....)))))....)))))..))))).... (-15.74 = -17.20 +   1.46)

alignment

secondary structure

dotplot

Window 8

Location	18,867,099 – 18,867,201
Length	102
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	82.70
Mean single sequence MFE	-32.52
Consensus MFE	-21.09
Energy contribution	-20.90
Covariance contribution	-0.19
Combinations/Pair	1.11
Mean z-score	-1.84
Structure conservation index	0.65
SVM decision value	0.31
SVM RNA-class probability	0.683621
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18867099 102 + 27905053
UGGCACCGCAUUCGGUGGAGCCCACUUCCAAUUUU-----CAGUACCAAACUGGUGCGGGGGUGGGGGGGAACGCGACCACCGCAGUAUGGGGCCAAAAAAAUUGAU
((((.(((.(((((((((..(((((((((......-----..(((((.....)))))))))))))).(....)....)))))).))).))).))))........... ( -42.90)
>DroSec_CAF1 91979 96 + 1
UGGCACCGCAUUCGGUGGAGCCCACU-CCAAUUUU-----UAGUACCAAAGUG-----GGGGAUGUGGGGAACGCGACCACCGCAGUAUGGGGCCAAAAAAAUUGAU
((((.(((.(((((((((..((((((-((.(((((-----.......))))).-----..))).)))))(....)..)))))).))).))).))))........... ( -33.20)
>DroEre_CAF1 94337 85 + 1
UGGCACCGCACUCGGUGCAACCCACU-CCAAUUUU-----UAGUACCGAAC---------------GGGGAACGCGACCACCGCAGUAUGGGGCCAAA-AAAUUGAU
..((((((....))))))........-.(((((((-----(.(..(((.((---------------.(....)(((.....))).)).)))..)..))-)))))).. ( -24.30)
>DroYak_CAF1 98669 93 + 1
UGGCAUCGCACUCGGUGGAGCCCACU-CCAAUUUUUUUUGUAGUACCGAAACG-------------GGGGAACGCGACCACCGCAGUAUGGGGCCAAAAAAAUUGAU
((((..((.(((((((((..((((((-.(((......))).))).(((...))-------------)))).......)))))).))).))..))))........... ( -29.70)
>consensus
UGGCACCGCACUCGGUGGAGCCCACU_CCAAUUUU_____UAGUACCAAACUG_____________GGGGAACGCGACCACCGCAGUAUGGGGCCAAAAAAAUUGAU
((((.(((.(((((((((..(((............................................))).......)))))).))).))).))))........... (-21.09 = -20.90 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:49 2006