Locus 2205

Sequence ID	3R_DroMel_CAF1
Location	6,291,694 – 6,291,785
Length	91
Max. P	0.966504

overview

Window 1

Location	6,291,694 – 6,291,785
Length	91
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	73.40
Mean single sequence MFE	-34.80
Consensus MFE	-22.27
Energy contribution	-23.27
Covariance contribution	1.00
Combinations/Pair	1.19
Mean z-score	-1.59
Structure conservation index	0.64
SVM decision value	1.13
SVM RNA-class probability	0.919461
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6291694 91 + 27905053
--------------GUUGGCGUGGAUUACCGGGCCAAAAGCGGAGCAGAGCUCCAA-AAGAACCCGGCUCGGG------------AUCGGGAUCCAAAGACAGGAGCAGAGCUCCCGA
--------------.(((((.(((....))).)))))..(.(((((...(((((..-..((.((((...))))------------.))((...)).......)))))...)))))).. ( -36.60)
>DroSec_CAF1 56783 91 + 1
--------------GUUGGCGUGGAUUACCGGGCCAAAAGCGGAGCAGAGCCCCAA-AAGAACCCGGCUCGGG------------AUCGGGAUCCAAAGACAGGAGCAGAGCUCCCGA
--------------.(((((.(((....))).)))))..(.(((((...(((((..-..((.((((...))))------------.))))).(((.......)))))...)))))).. ( -32.70)
>DroSim_CAF1 62363 91 + 1
--------------GUUGGCGUGGAUUACCGGGCCAAAAGCGGAGCAGAGCUCCAA-AAGAACCCGGCUCGGG------------AUCGGGAUCCAAAGACAGGAGCAGAGCUCCCGA
--------------.(((((.(((....))).)))))..(.(((((...(((((..-..((.((((...))))------------.))((...)).......)))))...)))))).. ( -36.60)
>DroEre_CAF1 62444 116 + 1
GUUGCCAGUUAACAGUUGGCGUGGAUUACCGGGCCAAAUGCGGAGCAGAGCACCAA-AAGAGCCCGGCUCGGGAUCGGGAUCGGGAU-GGGAUCCAAAGACAGGAGCAGCGCUCCCGA
((((((((.......))))).((((((.(((..((..((.(.((((.(.((.....-....)).).)))).).))..))..)))...-..))))))..))).(((((...)))))... ( -39.90)
>DroYak_CAF1 59510 105 + 1
GUUUCCA-------GUUGGCGUGGAUUACCGGGCCAAAUGCGGAGCAGAGCACCAA-AAGACCAC-----GGGAUGGGGAUCGGAAUCGGGAUCCAAAGACAGGAGCAGAGCUCCCGA
.....((-------.(((((.(((....))).))))).)).(((((...((.((..-....(((.-----....)))(((((........))))).......)).))...)))))... ( -34.50)
>DroAna_CAF1 61098 81 + 1
---------------UUGGCGUGGAUUACCCGGCCAAAA-CGGAGCCUGACUGAACGGAAAAUCGAGCUGGAG------------AC-G---ACCGAGUUCAGG-----AGCUCCCGA
---------------(((((.(((.....))))))))..-.(((((....((((((......(((.(.((...------------.)-)---.)))))))))).-----.)))))... ( -28.50)
>consensus
______________GUUGGCGUGGAUUACCGGGCCAAAAGCGGAGCAGAGCUCCAA_AAGAACCCGGCUCGGG____________AUCGGGAUCCAAAGACAGGAGCAGAGCUCCCGA
...............(((((.(((....))).)))))....(((((.(((((.............)))))......................(((.......))).....)))))... (-22.27 = -23.27 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	6,291,694 – 6,291,785
Length	91
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	73.40
Mean single sequence MFE	-33.53
Consensus MFE	-22.95
Energy contribution	-24.87
Covariance contribution	1.92
Combinations/Pair	1.16
Mean z-score	-1.70
Structure conservation index	0.68
SVM decision value	1.60
SVM RNA-class probability	0.966504
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6291694 91 - 27905053
UCGGGAGCUCUGCUCCUGUCUUUGGAUCCCGAU------------CCCGAGCCGGGUUCUU-UUGGAGCUCUGCUCCGCUUUUGGCCCGGUAAUCCACGCCAAC--------------
.(((((((...)))))))....(((((..((..------------..)).((((((((...-.((((((...)))))).....)))))))).))))).......-------------- ( -34.70)
>DroSec_CAF1 56783 91 - 1
UCGGGAGCUCUGCUCCUGUCUUUGGAUCCCGAU------------CCCGAGCCGGGUUCUU-UUGGGGCUCUGCUCCGCUUUUGGCCCGGUAAUCCACGCCAAC--------------
.(((((((...)))))))....(((((..((..------------..)).((((((((...-.((((((...)))))).....)))))))).))))).......-------------- ( -33.80)
>DroSim_CAF1 62363 91 - 1
UCGGGAGCUCUGCUCCUGUCUUUGGAUCCCGAU------------CCCGAGCCGGGUUCUU-UUGGAGCUCUGCUCCGCUUUUGGCCCGGUAAUCCACGCCAAC--------------
.(((((((...)))))))....(((((..((..------------..)).((((((((...-.((((((...)))))).....)))))))).))))).......-------------- ( -34.70)
>DroEre_CAF1 62444 116 - 1
UCGGGAGCGCUGCUCCUGUCUUUGGAUCCC-AUCCCGAUCCCGAUCCCGAGCCGGGCUCUU-UUGGUGCUCUGCUCCGCAUUUGGCCCGGUAAUCCACGCCAACUGUUAACUGGCAAC
((((((.((..((....))....(((((..-.....))))))).))))))((((((((...-..(((((........))))).)))))))).......((((.........))))... ( -39.40)
>DroYak_CAF1 59510 105 - 1
UCGGGAGCUCUGCUCCUGUCUUUGGAUCCCGAUUCCGAUCCCCAUCCC-----GUGGUCUU-UUGGUGCUCUGCUCCGCAUUUGGCCCGGUAAUCCACGCCAAC-------UGGAAAC
.(((((((...))))))).....(((((........)))))(((...(-----((((....-((((.(((.(((...)))...)))))))....))))).....-------))).... ( -32.10)
>DroAna_CAF1 61098 81 - 1
UCGGGAGCU-----CCUGAACUCGGU---C-GU------------CUCCAGCUCGAUUUUCCGUUCAGUCAGGCUCCG-UUUUGGCCGGGUAAUCCACGCCAA---------------
...((((((-----.((((((..(((---(-(.------------........)))))....))))))...)))))).-..(((((..((....))..)))))--------------- ( -26.50)
>consensus
UCGGGAGCUCUGCUCCUGUCUUUGGAUCCCGAU____________CCCGAGCCGGGUUCUU_UUGGAGCUCUGCUCCGCUUUUGGCCCGGUAAUCCACGCCAAC______________
.(((((((...)))))))..............................((((.(((((((....))))))).)))).....(((((..((....))..)))))............... (-22.95 = -24.87 +   1.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:49 2006