Locus 8500

Sequence ID	3L_DroMel_CAF1
Location	22,292,297 – 22,292,533
Length	236
Max. P	0.989789

overview

Window 2

Location	22,292,297 – 22,292,417
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.49
Mean single sequence MFE	-26.10
Consensus MFE	-23.24
Energy contribution	-23.30
Covariance contribution	0.06
Combinations/Pair	1.08
Mean z-score	-1.49
Structure conservation index	0.89
SVM decision value	0.33
SVM RNA-class probability	0.689520
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22292297 120 - 23771897
AAGUCGUAAACAUUAUUUCUAAAAAUUGCUUUUGUCGCAUUUCCUCGACAUAUUUGGCAGCAGUUCAAGACGCCAGAGCUGCUCUGGCGAACAAUUCCCACCACUUAGGAGGACAUAAAC
..((((....)....(((((((...(((((..(((((........))))).....)))))..........((((((((...))))))))...............))))))))))...... ( -28.50)
>DroSec_CAF1 50767 120 - 1
AAGUCGUAAACAUUAUUCCUAAAAAUUGCUUUUGUCGCAUUUCCUCGACAUAUUUGGCAGGAGUUCAAGACGCCAGAGCUGCUCUGGCCAACAAUUCCCACCACUUAGGAGAACAUAAAC
...............(((((((....((((..(((((........))))).....))))((((((......(((((((...)))))))....))))))......)))))))......... ( -30.50)
>DroEre_CAF1 49126 117 - 1
GAGUCGUAAACAUUAUUUCUAAAAAUAGCUUUUGUCGCAUUUUCUCGACACAAUUGGCAGCAGCUCAAGACGCCAGAG---CUCUGGCCAACAAUGCCCACCACUUAGAAGAACAUAAAC
...............(((((((..........(((((........)))))...(((((((.(((((.........)))---)))).))))).............)))))))......... ( -22.90)
>DroYak_CAF1 15160 117 - 1
GAGUCGUAAACAUUAUUUCUAAAAAUUGCUUUUGUCGCAUUUUCUCGACACAUUUGGCAGCAGUUCAAGACGCCAGAA---CUCUGGCCAACAAUUCUUACCACUUAGAAGAACAUAAAC
.........................(((((..(((((........))))).....)))))..((((.....(((((..---..)))))......((((........))))))))...... ( -22.50)
>consensus
AAGUCGUAAACAUUAUUUCUAAAAAUUGCUUUUGUCGCAUUUCCUCGACACAUUUGGCAGCAGUUCAAGACGCCAGAG___CUCUGGCCAACAAUUCCCACCACUUAGAAGAACAUAAAC
...............(((((((...(((((..(((((........))))).....)))))...........(((((((...)))))))................)))))))......... (-23.24 = -23.30 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	22,292,377 – 22,292,493
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.19
Mean single sequence MFE	-36.87
Consensus MFE	-33.78
Energy contribution	-33.65
Covariance contribution	-0.13
Combinations/Pair	1.11
Mean z-score	-2.42
Structure conservation index	0.92
SVM decision value	2.18
SVM RNA-class probability	0.989789
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22292377 116 - 23771897
UGCAGCCAAAUCCGUUUUCGAUGGCUGCGCCUAAAGUGCGGCAAGGGCAGCCAA----GGGAGGUAGACAACAGACAGCAAAGUCGUAAACAUUAUUUCUAAAAAUUGCUUUUGUCGCAU
.(((((((....((....)).))))))).......(((((((((((((((....----.((((((((......(((......))).......)))))))).....))))))))))))))) ( -41.72)
>DroSec_CAF1 50847 120 - 1
GGCAGCCAAAUCCGUUUUCGAUGGCUGCGCCUAAAGUGCGGCAAGGGUCACCAAAGGGGGGAGGUAGAAAACAGACAGCAAAGUCGUAAACAUUAUUCCUAAAAAUUGCUUUUGUCGCAU
.(((((((....((....)).))))))).......(((((((((((((..((....))(((((..........(((......)))..........))))).......))))))))))))) ( -38.25)
>DroEre_CAF1 49203 110 - 1
GGCAGCCAAAUCCGUUUUCAAUGGCUGCGCCUAAAAUGCGGCAAUGGCCGCCAGA---GGGAGC-------CAGACAACAGAGUCGUAAACAUUAUUUCUAAAAAUAGCUUUUGUCGCAU
.(((((((.............))))))).......(((((((((((((..((...---.)).))-------))(((......)))..........................))))))))) ( -32.62)
>DroYak_CAF1 15237 117 - 1
GGCAGCCAAAUCCGUUUUCAAUGGCUGCGCCUAAAAUGCGGCAAUGGCCGCCACC---GGGAGGUAGAUAACAGACAACAGAGUCGUAAACAUUAUUUCUAAAAAUUGCUUUUGUCGCAU
.(((((((.............))))))).......(((((((((.(((.......---.((((((((......(((......))).......)))))))).......))).))))))))) ( -34.90)
>consensus
GGCAGCCAAAUCCGUUUUCAAUGGCUGCGCCUAAAAUGCGGCAAGGGCCGCCAAA___GGGAGGUAGA_AACAGACAACAAAGUCGUAAACAUUAUUUCUAAAAAUUGCUUUUGUCGCAU
.(((((((.............))))))).......(((((((((((((..........(((((..........(((......)))..........))))).......))))))))))))) (-33.78 = -33.65 +  -0.13)

alignment

secondary structure

dotplot

Window 4

Location	22,292,417 – 22,292,533
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.61
Mean single sequence MFE	-38.28
Consensus MFE	-29.90
Energy contribution	-31.02
Covariance contribution	1.12
Combinations/Pair	1.07
Mean z-score	-2.01
Structure conservation index	0.78
SVM decision value	0.81
SVM RNA-class probability	0.856106
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22292417 116 - 23771897
AUGCAAUUUUCAGUUUGUUUUGGCUUUCUGAAAAGGACUUUGCAGCCAAAUCCGUUUUCGAUGGCUGCGCCUAAAGUGCGGCAAGGGCAGCCAA----GGGAGGUAGACAACAGACAGCA
............(((((((...(((((((((((((((.((((....))))))).)))))..((((((((((........)))....))))))).----)))))))....))))))).... ( -37.20)
>DroSec_CAF1 50887 120 - 1
AUGCAAUUUUCAGUUUGUUUUGGCUUUCUGAAAAGGACUUGGCAGCCAAAUCCGUUUUCGAUGGCUGCGCCUAAAGUGCGGCAAGGGUCACCAAAGGGGGGAGGUAGAAAACAGACAGCA
............(((((((((.(((((((((((((((.((((...)))).))).)))))(((.(((((((.....)))))))....))).((....)))))))))..))))))))).... ( -39.50)
>DroEre_CAF1 49243 110 - 1
AUGCAAUUUUCAGUUUGUUUUGGCUUUCCGAACAGGACUUGGCAGCCAAAUCCGUUUUCAAUGGCUGCGCCUAAAAUGCGGCAAUGGCCGCCAGA---GGGAGC-------CAGACAACA
............(((.((((.((((((((.....)))....(((((((.............))))))).(((.....(((((....)))))...)---))))))-------)))))))). ( -37.22)
>DroYak_CAF1 15277 117 - 1
AUGCAAUUUUCAGUUUGUUUUGGCUUUCUGAACAGGACUUGGCAGCCAAAUCCGUUUUCAAUGGCUGCGCCUAAAAUGCGGCAAUGGCCGCCACC---GGGAGGUAGAUAACAGACAACA
............(((((((...((((((((...(((.....(((((((.............))))))).))).....(((((....)))))...)---)))))))....))))))).... ( -39.22)
>consensus
AUGCAAUUUUCAGUUUGUUUUGGCUUUCUGAAAAGGACUUGGCAGCCAAAUCCGUUUUCAAUGGCUGCGCCUAAAAUGCGGCAAGGGCCGCCAAA___GGGAGGUAGA_AACAGACAACA
............(((((((...(((((((....(((.....(((((((.............))))))).))).....(((((....))))).......)))))))....))))))).... (-29.90 = -31.02 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:17:13 2006