Locus 1062

Sequence ID	3L_DroMel_CAF1
Location	3,113,608 – 3,113,738
Length	130
Max. P	0.639156

overview

Window 3

Location	3,113,608 – 3,113,715
Length	107
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	76.89
Mean single sequence MFE	-35.32
Consensus MFE	-21.37
Energy contribution	-20.23
Covariance contribution	-1.13
Combinations/Pair	1.50
Mean z-score	-1.46
Structure conservation index	0.61
SVM decision value	0.20
SVM RNA-class probability	0.632231
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3113608 107 - 23771897
CGCAGAGUGUUUGGAGCCAAGCGCACGAUUAUAAUGGGCCUAGCCCUGGAAAUCGUGCAGCUGCUGUGGUACGGCUUUGGCAGUCAAAAGUGGUGAGU-AAUA---A-AUAU
(((((((((((((....)))))((((((((.(...((((...))))..).)))))))).))).))))).(((.(((((........))))).)))...-....---.-.... ( -38.40)
>DroVir_CAF1 2676 109 - 1
UGCAGAGUCUUUGGCGCCAAGCGCACUAUCAUUGUGGGCCUAGCCCUCGAGUUGGUUCAACUGCUUUGGUACGGCCUGGGCAGUCAGAAGUGGUAAGU-CGAAGCCU-GAG-
..(((.(.(((((((((((..((.((((...(((.((((...)))).)))..)))).).((((((..((.....))..))))))..)...))))..))-))))))))-)..- ( -38.50)
>DroGri_CAF1 514 112 - 1
UGCAGAGUCUUUGGCGCCAAGCGCACCAUCAUUAUGGGCCUAGCCCUGGAGAUGAUUCAACUGCUUUGGUAUGGCCUGGGCAGUGAAAAGUGGUAAGCACAAAGCCAUUAUA
......(.(((((((((...))))(((((((((..((((...))))....)))))((((.(((((..((.....))..)))))))))...)))).....))))).)...... ( -36.10)
>DroEre_CAF1 756 103 - 1
CUCAGAGUGUUUGGAGCCAAGCGCACGAUCAUAAUGGGCCUAGCCCUGGAAAUCGUGCAGCUGCUGUGGUACGGCUUUGGCAGUCAAAAGUGGUAAGU-AAUA--------U
....((.((.(..(((((.((((((((((......((((...)))).....))))))).)))((....))..)))))..))).)).............-....--------. ( -34.40)
>DroWil_CAF1 745 107 - 1
UGCAGAGUAUUUGGAGCCAAACGUACAAUUAUUGUGGGCCUGGCUCUGGAAAUUGUUCAGCUGUUGUGGUAUGGCUUCGGUAGUCAAAAGUGGUAAGU-GCCA---U-UUAC
((.(.(((.((..((((((..(.((((.....)))).)..))))))..)).))).).))((((..(.((.....)).)..))))...(((((((....-))))---)-)).. ( -30.30)
>DroAna_CAF1 730 105 - 1
CGCAGGACAUUUGGAGCCAAGCGCACGAUCAUUAUGGGCCUAGCCCUCGAAAUGAUCCAGAUGCUGUGGUAUGGCUUUGGUAGCCAAAAAUGGUAAGU-CGCA---G-AU--
.((..(((..(..((((((.((.((((((((((..((((...))))....)))))))........))))).))))))..)..((((....))))..))-))).---.-..-- ( -34.20)
>consensus
CGCAGAGUAUUUGGAGCCAAGCGCACGAUCAUUAUGGGCCUAGCCCUGGAAAUGGUUCAGCUGCUGUGGUACGGCUUUGGCAGUCAAAAGUGGUAAGU_CAAA___A_AU__
...............((((...(.((((((.....((((...))))....)))))).).(((((((.((.....)).)))))))......)))).................. (-21.37 = -20.23 +  -1.13)

alignment

secondary structure

dotplot

Window 4

Location	3,113,637 – 3,113,738
Length	101
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	80.71
Mean single sequence MFE	-29.00
Consensus MFE	-22.25
Energy contribution	-21.70
Covariance contribution	-0.55
Combinations/Pair	1.32
Mean z-score	-1.28
Structure conservation index	0.77
SVM decision value	0.22
SVM RNA-class probability	0.639156
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3113637 101 + 23771897
AAAGCCGUACCACAGCAGCUGCACGAUUUCCAGGGCUAGGCCCAUUAUAAUCGUGCGCUUGGCUCCAAACACUCUGC--GAAA-GAAGCAUGUAA-------UUAG----CCACC
...((.(.....).))(((.((((((((....((((...)))).....)))))))))))(((((....(((..((.(--....-).))..)))..-------..))----))).. ( -31.70)
>DroPse_CAF1 799 110 + 1
CAAGCCGUACCACAGCAGCUGUACGAUUUCCAAGGCCAGGCCCACAAUGAUCGUUCGCUUGGCGCCAAACACUCUGAAGGACA-GAAACAGAUGAC----GAUUAGGAUUCCGAG
..(((.((......)).)))...((...(((...(((((((..((.......))..))))))).........((((.....))-))..........----.....)))...)).. ( -22.90)
>DroGri_CAF1 548 106 + 1
CAGGCCAUACCAAAGCAGUUGAAUCAUCUCCAGGGCUAGGCCCAUAAUGAUGGUGCGCUUGGCGCCAAAGACUCUGC--AA-G-AACACAGAUUAGUGGGGAUUAC----AAAU-
..((.....))..............((((((((((((((((((((....))))...))))))).))......((((.--..-.-....))))....)))))))...----....- ( -26.90)
>DroSec_CAF1 2625 101 + 1
AAAGCCGUACCACAGCAGCUGCACGAUUUCCAGGGCUAGGCCCAUUAUGAUCGUGCGCUUGGCUCCAAAUACUCUGC--GAAA-GAAGCAUGUAA-------UUAG----CCACU
...((.(.....).))(((.((((((((....((((...)))).....)))))))))))(((((..((.(((..(((--....-...))).))).-------))))----))).. ( -30.80)
>DroSim_CAF1 777 102 + 1
AAAGCCGUACCACAGCAGCUGCACGAUCUCCAGGGCUAGGCCCAUUAUGAUCGUGCGCUUGGCUCCAAACACUCUGC--GAAAAAAAGCAUGUAA-------UUAG----CCACU
...((.(.....).))(((.((((((((....((((...)))).....)))))))))))(((((....(((...(((--........))))))..-------..))----))).. ( -32.90)
>DroEre_CAF1 781 101 + 1
AAAGCCGUACCACAGCAGCUGCACGAUUUCCAGGGCUAGGCCCAUUAUGAUCGUGCGCUUGGCUCCAAACACUCUGA--GAAA-GAUGCAUGUAA-------UUAG----CCACU
...((.(.....).))(((.((((((((....((((...)))).....)))))))))))(((((....(((.(((..--...)-))....)))..-------..))----))).. ( -28.80)
>consensus
AAAGCCGUACCACAGCAGCUGCACGAUUUCCAGGGCUAGGCCCAUUAUGAUCGUGCGCUUGGCUCCAAACACUCUGC__GAAA_GAAGCAUGUAA_______UUAG____CCACU
...((((.........(((.((((((((....((((...)))).....))))))))))))))).................................................... (-22.25 = -21.70 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:05 2006