Locus 6305

Sequence ID	2R_DroMel_CAF1
Location	19,753,943 – 19,754,082
Length	139
Max. P	0.779710

overview

Window 7

Location	19,753,943 – 19,754,042
Length	99
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.02
Mean single sequence MFE	-21.03
Consensus MFE	-17.57
Energy contribution	-17.82
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.84
SVM decision value	0.55
SVM RNA-class probability	0.779710
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19753943 99 + 20766785
CCAUACCCAUACCAAUUCCC------AUUCCCACUUC-CAUUCCCGA--------------UUCCCAUUCCCAGUGGCCCCGUGCGUAUCCUUCCACGCCAUGCCGCCAAUCAAGGGGAG
....................------...........-.........--------------.((((........((((..(((((((........))).))))..))))......)))). ( -18.44)
>DroSec_CAF1 6730 100 + 1
CCGUUCCCAUUCCCACUUCC------AUUCCCAAUUCCCAUUCCCAA--------------UUCCCAUUCUCAGUGGCCCCGUGCGUAUCCUUCCACGCCAUGCCGCCAAUCAAGGGGAG
....................------.....................--------------.((((........((((..(((((((........))).))))..))))......)))). ( -18.44)
>DroEre_CAF1 6863 119 + 1
CUAUUUCCAUACCCAUUCCCACUUAUAUUCCCGCUUC-CAUUCGCAAUUCCGAAUUCCCAUUUCCCAUUCCCAGUGGCCCCGUGCGAAUCCUUCCACGCCAUGCCGCCAAUCAAGGGGAG
................((((.(((.............-.(((((......)))))..................(((((..((((.((.....))))))....))))).....))))))). ( -21.80)
>DroYak_CAF1 9628 105 + 1
CCACUGCCAUGCCCACUGCC------AUUCCCACUUC-CAUUCCCAAUA-------CCCA-UUCCCAUUGGCAGUGGCCCCGUGCGUAUCCUUCCACGCCAUGCCGCCAAUCAAGGGGAG
.........(.(((((((((------(..........-...........-------....-.......)))))))(((..(((((((........))).))))..)))......))).). ( -25.45)
>consensus
CCAUUCCCAUACCCACUCCC______AUUCCCACUUC_CAUUCCCAA______________UUCCCAUUCCCAGUGGCCCCGUGCGUAUCCUUCCACGCCAUGCCGCCAAUCAAGGGGAG
..............................................................((((........((((..(((((((........))).))))..))))......)))). (-17.57 = -17.82 +   0.25)

alignment

secondary structure

dotplot

Window 8

Location	19,753,976 – 19,754,082
Length	106
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.00
Mean single sequence MFE	-25.17
Consensus MFE	-21.92
Energy contribution	-22.16
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.87
SVM decision value	0.47
SVM RNA-class probability	0.748835
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19753976 106 + 20766785
UUCCCGA--------------UUCCCAUUCCCAGUGGCCCCGUGCGUAUCCUUCCACGCCAUGCCGCCAAUCAAGGGGAGGACGCAUUAUACUUUUGCGCAAACAAAUCAUAAAUAUUAA
.....((--------------((.((.(((((..((((..(((((((........))).))))..)))).....))))))).((((.........))))......))))........... ( -25.60)
>DroSec_CAF1 6764 106 + 1
UUCCCAA--------------UUCCCAUUCUCAGUGGCCCCGUGCGUAUCCUUCCACGCCAUGCCGCCAAUCAAGGGGAGGACGCAUUAUACUUUUGCGCAAACAAAUCAUAAAUAUUAA
.(((...--------------.((((........((((..(((((((........))).))))..))))......)))))))((((.........))))..................... ( -23.24)
>DroEre_CAF1 6902 120 + 1
UUCGCAAUUCCGAAUUCCCAUUUCCCAUUCCCAGUGGCCCCGUGCGAAUCCUUCCACGCCAUGCCGCCAAUCAAGGGGAGGACGCAUUAUACUUUUGCGCAAACAAAUCAUAAAUAUUCA
...........(((((((...(((((.......(((((..((((.((.....))))))....))))).......))))))))((((.........))))................)))). ( -24.74)
>DroYak_CAF1 9661 112 + 1
UUCCCAAUA-------CCCA-UUCCCAUUGGCAGUGGCCCCGUGCGUAUCCUUCCACGCCAUGCCGCCAAUCAAGGGGAGGACGCAUUAUACUUUUGCGCAAACAAAUCAUAAAUAUUAA
.........-------.((.-(((((((((((.(((((...(((.(.......)))))))))...))))))...))))))).((((.........))))..................... ( -27.10)
>consensus
UUCCCAA______________UUCCCAUUCCCAGUGGCCCCGUGCGUAUCCUUCCACGCCAUGCCGCCAAUCAAGGGGAGGACGCAUUAUACUUUUGCGCAAACAAAUCAUAAAUAUUAA
.....................(((((........((((..(((((((........))).))))..))))......)))))(.((((.........))))).................... (-21.92 = -22.16 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:51 2006