Locus 4327

Sequence ID	2L_DroMel_CAF1
Location	12,387,942 – 12,388,058
Length	116
Max. P	0.934192

overview

Window 7

Location	12,387,942 – 12,388,058
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	69.34
Mean single sequence MFE	-32.98
Consensus MFE	-18.91
Energy contribution	-19.98
Covariance contribution	1.06
Combinations/Pair	1.33
Mean z-score	-1.77
Structure conservation index	0.57
SVM decision value	1.23
SVM RNA-class probability	0.934192
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12387942 116 + 22407834
GUUUUGAUAAGUCUUAUGGCAGCGGCAAGUCGGCUUACAGCAUCAGAAUA-AUGACGCGCACUUAAGCCGCCUUCGCAUGUCCACCC---GACUAUCAAACCACCCACUUUACAAACCAC
(.(((((((.(((...(((((((((..((.(((((((..((.(((.....-.))).)).....))))))).)))))).)).)))...---)))))))))).).................. ( -32.70)
>DroPse_CAF1 294565 105 + 1
-----GAUAAGUUUUAUGGCAACUGAGAUGCGGCUUACAGCAUCAGCAUAAAUGACGCGCACUUAAGCCGUGUCC-------CGGCC---GACCACCUUGAGGCCCGGACAGGCUCCUAC
-----.....((((((.(....)))))))((((((((..((.(((.......))).)).....))))))))((((-------.((((---...........)))).)))).......... ( -33.50)
>DroAna_CAF1 199175 110 + 1
GUUUUGAUAAGUUUUAUGGCAACUGCGAGGCGGCUUACAGCAUCAGAAUA-AUGACGCGCACUUAAGCUGCUGCCGCAUCGCCAACCACCAGCCGCCAAACCACC---------AACCAC
................((((...((((.(((((((((..((.(((.....-.))).)).....)))))))))..))))..)))).....................---------...... ( -28.80)
>DroPer_CAF1 297001 105 + 1
-----GAUAAGUUUUAUGGGAACUGAGAUGCGGCUUACAGCAUCAGCAUAAAUGACGCGCACUUAAGCCGUGUCC-------CGGCC---GACCACCUUGAGGCCCGGACAGGCUCCUAC
-----...........(((((.(((.(((((((((((..((.(((.......))).)).....)))))))))))(-------(((((---...........)).)))).)))..))))). ( -36.90)
>consensus
_____GAUAAGUUUUAUGGCAACUGAGAGGCGGCUUACAGCAUCAGAAUA_AUGACGCGCACUUAAGCCGCGUCC_______CAGCC___GACCACCAAAACACCCGGACAGGCAACCAC
..........(((((((((.......(((((((((((..((.(((.......))).)).....))))))))))).........((.......)).)))))))))................ (-18.91 = -19.98 +   1.06)

alignment

secondary structure

dotplot

Window 8

Location	12,387,942 – 12,388,058
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	69.34
Mean single sequence MFE	-40.67
Consensus MFE	-20.17
Energy contribution	-21.18
Covariance contribution	1.00
Combinations/Pair	1.37
Mean z-score	-2.03
Structure conservation index	0.50
SVM decision value	1.10
SVM RNA-class probability	0.914948
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12387942 116 - 22407834
GUGGUUUGUAAAGUGGGUGGUUUGAUAGUC---GGGUGGACAUGCGAAGGCGGCUUAAGUGCGCGUCAU-UAUUCUGAUGCUGUAAGCCGACUUGCCGCUGCCAUAAGACUUAUCAAAAC
....................((((((((((---..((((.((.(((.((((((((((.....((((((.-.....))))))..))))))).)))..)))))))))..))).))))))).. ( -41.30)
>DroPse_CAF1 294565 105 - 1
GUAGGAGCCUGUCCGGGCCUCAAGGUGGUC---GGCCG-------GGACACGGCUUAAGUGCGCGUCAUUUAUGCUGAUGCUGUAAGCCGCAUCUCAGUUGCCAUAAAACUUAUC-----
...(..((((....))))..)...((((.(---(((.(-------(((..(((((((.....((((((.......))))))..)))))))..)))).))))))))..........----- ( -38.40)
>DroAna_CAF1 199175 110 - 1
GUGGUU---------GGUGGUUUGGCGGCUGGUGGUUGGCGAUGCGGCAGCAGCUUAAGUGCGCGUCAU-UAUUCUGAUGCUGUAAGCCGCCUCGCAGUUGCCAUAAAACUUAUCAAAAC
.((((.---------(((....((((((((((.(((.(((..((((((.((.((......))))((((.-.....)))))))))).)))))).).)))))))))....))).)))).... ( -44.40)
>DroPer_CAF1 297001 105 - 1
GUAGGAGCCUGUCCGGGCCUCAAGGUGGUC---GGCCG-------GGACACGGCUUAAGUGCGCGUCAUUUAUGCUGAUGCUGUAAGCCGCAUCUCAGUUCCCAUAAAACUUAUC-----
...(((((.(((((.((((...........---)))).-------)))))(((((((.....((((((.......))))))..))))))).......))))).............----- ( -38.60)
>consensus
GUAGGAGCCUGUCCGGGCCGCAAGGUGGUC___GGCCG_______GGACACGGCUUAAGUGCGCGUCAU_UAUGCUGAUGCUGUAAGCCGCAUCGCAGUUGCCAUAAAACUUAUC_____
...............((((((....((((.....)))).....((((...(((((((.....((((((.......))))))..)))))))..)))).))))))................. (-20.17 = -21.18 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:08 2006