Locus 4056

Sequence ID	2R_DroMel_CAF1
Location	13,382,168 – 13,382,303
Length	135
Max. P	0.901110

overview

Window 4

Location	13,382,168 – 13,382,266
Length	98
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	78.09
Mean single sequence MFE	-18.67
Consensus MFE	-11.91
Energy contribution	-12.61
Covariance contribution	0.69
Combinations/Pair	1.07
Mean z-score	-1.90
Structure conservation index	0.64
SVM decision value	1.02
SVM RNA-class probability	0.901110
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13382168 98 + 20766785
AUAUAAA-U-AA--UUGAACUUACCUGCUUCCUUUUCGCCAUCCUUGUCCUUGGCAUUCACUGAUGCAGCCGAUUCGUUUGCAUCACCAUCGGCAUCAUCAA
.......-.-..--...........((((........((((..........))))......((((((((.((...)).)))))))).....))))....... ( -18.00)
>DroVir_CAF1 1751 94 + 1
---UUCAAUU--UUUAUUACUCACCUGG---CUUUUCAGCAUCCUUCUCAUUGGCAUUGACCGAUGCAGUCGAUUCAUUUGGCUCACCAUCGGCCUCAUCAA
---.(((((.--...............(---((....)))..((........)).)))))((((((.((((((.....))))))...))))))......... ( -17.00)
>DroGri_CAF1 1 83 + 1
----------------UUACUCACCUGG---CUUAUCAGCAUCCUUAUCCUUGGCAUUGACCGAUGCGCCCGAUUCAUUUGCCUCUCCAUCGGCCUCAUCAA
----------------........(.((---(.((((.(((.((........))...)).).)))).))).)........(((........)))........ ( -12.70)
>DroSec_CAF1 1 85 + 1
-----------------AACUUACCUGCUUCCUUUUCGCCAUCUUUGUCCUUGGCAUUCACUGAUGCAGCCGAUUCGUUUGCAUCACCAUCGGCAUCAUCAA
-----------------........((((........((((..........))))......((((((((.((...)).)))))))).....))))....... ( -18.00)
>DroSim_CAF1 8 98 + 1
GUUUAAA-U-GA--UUGAACUUACCUGCUUCUUUUUCGCCAUCCUUGUCCUUGGCAUUCACUGAUGCAGCCGAUUCGUUUGCAUCACCAUCGGCAUCAUCAA
((((((.-.-..--)))))).....((((........((((..........))))......((((((((.((...)).)))))))).....))))....... ( -20.20)
>DroYak_CAF1 8 98 + 1
AUAUAUG-U-GA--AUGAACUCACCUGGUUCCUUAUCGCCAUCCUUGUCCUUGGCAUUCACUGAUGCAGCCGAUUCGUUUGCAUCUCCAUCGGCAUCAUCAA
......(-(-((--(((((((.....)))))......((((..........))))))))))(((((..((((((..............))))))..))))). ( -26.14)
>consensus
___UA_A_U_____UUGAACUCACCUGCUUCCUUUUCGCCAUCCUUGUCCUUGGCAUUCACUGAUGCAGCCGAUUCGUUUGCAUCACCAUCGGCAUCAUCAA
.....................................((((..........)))).......((((..((((((..............))))))..)))).. (-11.91 = -12.61 +   0.69)

alignment

secondary structure

dotplot

Window 5

Location	13,382,192 – 13,382,303
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.25
Mean single sequence MFE	-21.42
Consensus MFE	-14.25
Energy contribution	-14.14
Covariance contribution	-0.11
Combinations/Pair	1.19
Mean z-score	-1.83
Structure conservation index	0.67
SVM decision value	0.43
SVM RNA-class probability	0.734146
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13382192 111 + 20766785
UUCCUUUUCGCCAUCCUUGUCC---UUGGCA---UUCACUGAUGCAGCCGAUUCGUUUGCAUCACCAUCGGCAUCAUCAAUAUCGGAAUCCUCUUCCUCGUCCUCCUCGCC---AGCCUC
......................---(((((.---.....(((((..((((((..((.......)).))))))..))))).....((((.....))))...........)))---)).... ( -22.30)
>DroVir_CAF1 1774 108 + 1
---CUUUUCAGCAUCCUUCUCA---UUGGCA---UUGACCGAUGCAGUCGAUUCAUUUGGCUCACCAUCGGCCUCAUCAAUAUCGGAAUCCUCGUCCUCAUCGUCAUCGCC---GCCCUC
---...................---..(((.---.((((.((((..(((((......(((....))))))))..))))......(((.......))).....))))..)))---...... ( -22.70)
>DroGri_CAF1 13 111 + 1
---CUUAUCAGCAUCCUUAUCC---UUGGCA---UUGACCGAUGCGCCCGAUUCAUUUGCCUCUCCAUCGGCCUCAUCAAUAUCGGAAUCCUCAUCCUCAUCGUCGUCGCCAGCGCCUUC
---...................---(((((.---.((((.((((.(.(((((..............))))).).))))......(((.......))).....))))..)))))....... ( -21.94)
>DroEre_CAF1 38 111 + 1
UUCCUUUUCGCCAUCCUUGUCC---UUGGCG---UUUACUGAUGCAGCCGAUUCGUUUGCAUCUCCAUCGGCAUCAUCAAUAUCGGAAUCCUCAUCCUCGUCGUCCUCGCC---UCCUUC
((((....(((((.........---.)))))---.....(((((..((((((..............))))))..))))).....)))).......................---...... ( -22.24)
>DroMoj_CAF1 37 114 + 1
---CUUCUCAGCAUCCUUCUCAUCCUUGGCAUUAUUGACAGAUGCAGCCGAUUCAUUUGGAUCACCAUCGGCUUCAUCAAUAUCUGAAUCUUCAUCCUCAUCCUCAUCGCC---GCCCUC
---........................(((..........((((.((((((......(((....))))))))).))))......(((....)))..............)))---...... ( -20.70)
>DroAna_CAF1 38 111 + 1
GCCCUUUUCGCCGUCCUUGUCA---UUGGCA---UUUACUGAGGCGGUCGAUUCAUUAGCCUCACCAUCAGCCUCCUCAAUAUCGGAAUCUUCAUCUUCAUCGUCCUCGCC---ACCUUC
......................---.((((.---.....(((((.(((.(((..............))).))).))))).....(((................)))..)))---)..... ( -18.63)
>consensus
___CUUUUCACCAUCCUUGUCA___UUGGCA___UUGACUGAUGCAGCCGAUUCAUUUGCAUCACCAUCGGCCUCAUCAAUAUCGGAAUCCUCAUCCUCAUCGUCCUCGCC___GCCCUC
...........................(((..........((((..((((((..............))))))..))))......(((.......)))...........)))......... (-14.25 = -14.14 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:41 2006