Locus 10121

Sequence ID	3R_DroMel_CAF1
Location	27,146,089 – 27,146,181
Length	92
Max. P	0.960911

overview

Window 9

Location	27,146,089 – 27,146,181
Length	92
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	78.53
Mean single sequence MFE	-20.24
Consensus MFE	-9.04
Energy contribution	-9.00
Covariance contribution	-0.04
Combinations/Pair	1.21
Mean z-score	-2.49
Structure conservation index	0.45
SVM decision value	1.52
SVM RNA-class probability	0.960911
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27146089 92 + 27905053
GCAAA-CUU-UGCAGUAGCAGUGGCAAAAUGGCAAACUGGCAAAAAA------GAAAAUGAAAAGCGAGGAAAGGCCACAAUGAGAGCUGCUAAUAGCUG
.....-...-.((..(((((((..((...((((...((.((......------...........)).)).....))))...))...)))))))...)).. ( -22.73)
>DroSim_CAF1 50166 92 + 1
GAAAA-CUG-UGCAGUAGCAUUGGCCAAAUGGCAAACUGGCAAAAAA------GAAAAUGAAAAGCGAGGAAAGGCCACAAUGAGAGCUGCUAAUAGCUG
.....-(((-((((((..((((((((....)))....((((......------.....(....)..........)))))))))...)))))..))))... ( -22.20)
>DroEre_CAF1 48479 97 + 1
GAAAA-CUU-UGCAGUAGCAGUGGCAAAAUGGAA-AAUGGCAAAAAAGAAGUUGAAAAUGAAUAGCGAGGAAAGGCCACAAUGAGAGCUGCUAAUAGCUG
.....-...-.((..(((((((..((...(....-).((((.........((((........))))........))))...))...)))))))...)).. ( -17.43)
>DroYak_CAF1 50647 84 + 1
GAAAA-CUUUUCCAGUAGCAGUGGCAAAAU--------GGCAAAAA-------GAAAAUGAAAAGCGAGGAAAGGCCACAAUGAGAGCUGCUAAUAGCUG
.....-......((((((((((..((...(--------(((.....-------.....(....)..........))))...))...))))))....)))) ( -16.85)
>DroAna_CAF1 52731 83 + 1
AAAAAGUUU-UCCAGUAGCGGCAGCAG----UUAUAGCCGCUAAAAA------U------AAAACUGAGGAAAGGCAACAAUGAGAGUUGCUAAUAGCUG
....(((((-(....(((((((.....----.....)))))))....------.------)))))).......((((((.......))))))........ ( -22.00)
>consensus
GAAAA_CUU_UGCAGUAGCAGUGGCAAAAUGGCA_ACUGGCAAAAAA______GAAAAUGAAAAGCGAGGAAAGGCCACAAUGAGAGCUGCUAAUAGCUG
............((((((((((.((..............))...........................((.....)).........))))))....)))) ( -9.04 =  -9.00 +  -0.04)

alignment

secondary structure

dotplot

Window 0

Location	27,146,089 – 27,146,181
Length	92
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	78.53
Mean single sequence MFE	-16.96
Consensus MFE	-6.05
Energy contribution	-6.49
Covariance contribution	0.44
Combinations/Pair	1.08
Mean z-score	-2.24
Structure conservation index	0.36
SVM decision value	0.83
SVM RNA-class probability	0.861098
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27146089 92 - 27905053
CAGCUAUUAGCAGCUCUCAUUGUGGCCUUUCCUCGCUUUUCAUUUUC------UUUUUUGCCAGUUUGCCAUUUUGCCACUGCUACUGCA-AAG-UUUGC
..((...((((((....((..(((((.....((.((...........------......)).))...)))))..))...))))))..)).-...-..... ( -18.83)
>DroSim_CAF1 50166 92 - 1
CAGCUAUUAGCAGCUCUCAUUGUGGCCUUUCCUCGCUUUUCAUUUUC------UUUUUUGCCAGUUUGCCAUUUGGCCAAUGCUACUGCA-CAG-UUUUC
..((...(((((....(((..(((((.....((.((...........------......)).))...))))).)))....)))))..)).-...-..... ( -16.43)
>DroEre_CAF1 48479 97 - 1
CAGCUAUUAGCAGCUCUCAUUGUGGCCUUUCCUCGCUAUUCAUUUUCAACUUCUUUUUUGCCAUU-UUCCAUUUUGCCACUGCUACUGCA-AAG-UUUUC
..((...((((((....((..((((.........((.......................))....-..))))..))...))))))..)).-...-..... ( -12.96)
>DroYak_CAF1 50647 84 - 1
CAGCUAUUAGCAGCUCUCAUUGUGGCCUUUCCUCGCUUUUCAUUUUC-------UUUUUGCC--------AUUUUGCCACUGCUACUGGAAAAG-UUUUC
...(((.((((((....((..(((((.....................-------.....)))--------))..))...)))))).))).....-..... ( -15.77)
>DroAna_CAF1 52731 83 - 1
CAGCUAUUAGCAACUCUCAUUGUUGCCUUUCCUCAGUUUU------A------UUUUUAGCGGCUAUAA----CUGCUGCCGCUACUGGA-AAACUUUUU
.........(((((.......)))))........((((((------.------....(((((((.....----.....)))))))....)-))))).... ( -20.80)
>consensus
CAGCUAUUAGCAGCUCUCAUUGUGGCCUUUCCUCGCUUUUCAUUUUC______UUUUUUGCCAGU_UGCCAUUUUGCCACUGCUACUGCA_AAG_UUUUC
(((....(((((.........(((((.................................................)))))))))))))............ ( -6.05 =  -6.49 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:49:19 2006